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R

Views: 4031
Kernel: R
options(jupyter.plot_mimetypes ='image/png')

Step1

setwd("~/Autumn2016/Week5/data_wk_5")

load("estrogen_data.RDA")
ls()
library(affy)
[1] "affybatch.estrogen"
Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. 
show(affybatch.estrogen)
AffyBatch object size of arrays=640x640 features (19 kb) cdf=HG_U95Av2 (12625 affyids) number of samples=8 number of genes=12625 annotation=hgu95av2 notes=

Step 2

pData(affybatch.estrogen)
estrogen time.h low10-1.cel absent 10 low10-2.cel absent 10 high10-1.cel present 10 high10-2.cel present 10 low48-1.cel absent 48 low48-2.cel absent 48 high48-1.cel present 48 high48-2.cel present 48

Step3

eset_rma<-rma(affybatch.estrogen)
Background correcting Normalizing Calculating Expression 
e_rma<-exprs(eset_rma)
show(e_rma)
low10-1.cel low10-2.cel high10-1.cel high10-2.cel 100_g_at 9.642896 9.741496 9.537036 9.353625 1000_at 10.398169 10.254362 10.003971 9.903528 1001_at 5.717613 5.881008 5.859563 5.954028 1002_f_at 5.512596 5.801807 5.571065 5.608132 1003_s_at 7.783927 8.007975 8.037999 7.835120 1004_at 7.289162 7.603670 7.488539 7.771506 1005_at 9.206737 8.993802 8.237894 8.338004 1006_at 5.387194 5.555903 5.407540 5.744037 1007_s_at 11.903336 11.744515 11.408794 11.527227 1008_f_at 10.119331 10.986646 10.830297 10.025093 1009_at 10.553067 10.500444 11.159834 11.048275 101_at 6.874924 6.685042 6.742094 7.088004 1010_at 7.710794 7.827522 7.861160 7.781537 1011_s_at 8.343790 7.946077 8.301511 8.048696 1012_at 5.085473 5.090197 5.010356 5.033141 1013_at 5.257827 5.157303 5.472129 4.840000 1014_at 8.915023 8.982987 9.060316 8.910991 1015_s_at 7.430635 7.558621 7.297271 7.625685 1016_s_at 5.432050 5.331180 5.512469 5.296041 1017_at 5.536575 5.302901 5.578643 5.167248 1018_at 7.502612 7.745897 7.514347 7.735576 1019_g_at 7.677789 7.785227 7.687340 7.568828 102_at 5.138951 5.027597 5.130461 5.025212 1020_s_at 10.680684 10.699885 10.229423 10.323437 1021_at 5.410298 5.409684 5.384937 5.560545 1022_f_at 5.084912 5.070868 4.859666 4.868026 1023_at 7.707297 7.814656 7.730263 7.914271 1024_at 8.470394 8.674475 8.176687 8.197421 1025_g_at 8.065307 8.008628 7.172242 6.960242 1026_s_at 8.553119 8.900618 8.836525 8.956549 1027_at 6.622867 6.827711 6.706468 6.876677 1028_at 6.430411 6.726031 7.041277 6.609983 1029_s_at 5.477172 5.621707 5.378969 5.686420 103_at 6.428133 6.666195 6.768352 6.597580 1030_s_at 10.512354 10.205326 10.270552 10.133657 1031_at 5.677651 5.552463 5.690350 5.685400 1032_at 8.432695 8.382068 8.278558 8.228841 1033_g_at 7.032555 7.202372 7.230408 7.463152 1034_at 9.760735 9.836141 9.177038 9.288894 1035_g_at 9.527874 9.542509 8.955074 9.002284 1036_at 4.830291 4.936907 4.932133 4.666825 1037_at 5.662725 5.472959 5.358285 5.161015 1038_s_at 5.901607 5.939607 5.555385 5.319171 1039_s_at 6.554662 6.330902 6.562333 6.317292 104_at 6.278339 6.640352 6.346205 6.783851 1040_s_at 6.083591 6.088750 6.265829 6.067649 1041_at 6.091283 6.055030 6.138264 5.711348 1042_at 5.101684 5.023568 4.995484 4.867035 1043_s_at 5.125010 5.279859 5.171048 5.164333 1044_s_at 7.070884 7.010306 6.814739 6.473785 1045_s_at 7.546898 7.425160 7.361178 7.440968 1046_at 7.002425 6.829167 6.571223 6.093217 1047_s_at 7.613787 7.737549 7.657278 7.926887 1048_at 5.966908 6.194431 5.910475 5.890035 1049_g_at 7.965777 8.187409 8.106571 8.281858 105_at 5.406687 5.264260 5.322083 5.249372 1050_at 4.710873 4.667297 4.629110 4.410434 1051_g_at 5.865866 5.964442 5.941349 6.017072 1052_s_at 8.612015 8.662713 8.148018 7.729578 1053_at 7.507444 7.705315 9.013984 8.881018 1054_at 5.229868 5.397207 6.000676 5.542477 1055_g_at 5.308277 5.542251 7.730258 7.180788 1056_s_at 5.267739 5.237133 5.112614 5.278732 1057_at 11.551935 11.500478 10.909403 10.817548 1058_at 6.386659 6.228106 6.466572 6.059320 1059_at 4.846094 4.904160 4.941990 4.851625 106_at 5.791639 5.835975 5.725784 5.665831 1060_g_at 6.861098 6.704402 6.650059 6.924016 1061_at 7.683161 7.653307 7.467129 7.774108 1062_g_at 5.473496 5.347484 5.325247 5.373388 1063_s_at 8.585360 8.462941 8.399407 8.434714 1064_at 6.521782 6.159743 6.664437 6.075673 1065_at 5.929698 5.665261 5.807332 5.775397 1066_at 6.790852 6.881369 6.709866 6.761865 1067_at 5.418343 5.545940 5.497581 5.868340 1068_g_at 8.771160 8.876110 8.738459 8.723423 1069_at 5.180554 4.943958 5.004046 5.190595 107_at 6.623105 6.639328 6.458863 6.640859 1070_at 6.000713 5.980001 5.892124 5.868670 1071_at 8.321911 8.460795 8.270695 8.301794 1072_g_at 9.257282 9.156745 8.963330 9.167749 1073_at 9.890934 9.677518 9.988729 9.699978 1074_at 8.351963 7.926189 8.207923 7.766612 1075_f_at 4.947796 4.875199 4.926694 4.796239 1076_at 5.216481 5.399137 4.984869 4.923780 1077_at 5.064383 4.713556 4.910584 4.802097 1078_at 6.990170 6.957151 6.856677 7.000882 1079_g_at 8.594940 8.569572 8.390710 8.542123 108_g_at 8.969312 9.019119 8.869007 8.941589 1080_s_at 5.214044 5.306904 5.330110 5.461090 1081_at 10.400582 10.357400 10.211228 10.307576 1082_at 6.756793 6.671383 7.050053 6.849051 1083_s_at 7.610101 7.822400 7.666960 7.715963 1084_at 6.414543 6.406852 6.277702 6.461941 1085_s_at 8.618845 8.557181 8.546399 8.568133 1086_at 5.991659 6.280078 5.964693 6.231882 1087_at 8.358315 8.290649 7.149234 7.269803 1088_at 4.532977 4.674389 4.755996 4.654147 1089_i_at 6.627093 6.690936 6.504123 6.682948 109_at 8.661940 8.708365 8.929839 8.964127 1090_f_at 5.213933 5.405831 5.326860 5.178819 1091_at 9.904281 9.916458 9.852487 9.908819 1092_at 9.976329 10.021783 9.955591 10.090141 1093_at 4.892422 4.922914 4.978306 5.004207 1094_g_at 6.437868 6.522975 6.570646 6.401655 1095_s_at 4.521111 4.560595 4.443716 4.558383 1096_g_at 6.962739 7.151345 7.049507 7.331554 1097_s_at 6.466293 6.541656 6.180189 6.291953 1098_at 4.598019 4.702192 4.589817 4.590442 1099_s_at 5.539282 5.664477 5.637878 5.610691 110_at 8.733122 8.744683 8.710860 8.691365 1100_at 10.176399 9.914695 10.315291 10.613700 1101_at 5.702536 5.718756 5.736056 5.900077 1102_s_at 7.118835 6.961711 6.838405 6.531897 1103_at 6.545946 6.507005 6.595136 6.393060 1104_s_at 11.183876 11.026823 10.853457 10.927425 1105_s_at 8.826797 8.835644 8.734926 8.667511 1106_s_at 7.600797 7.738826 7.601277 7.622805 1107_s_at 13.552806 13.706690 13.386566 13.184111 1108_s_at 7.800683 7.769756 7.664077 7.949223 1109_s_at 8.581079 8.671189 8.450319 8.502193 111_at 8.790229 8.839021 8.592054 8.564246 1110_at 6.028269 6.259788 6.201889 6.058553 1111_at 5.825284 5.879724 5.708296 5.847541 1112_g_at 7.328844 7.481105 7.319070 7.523739 1113_at 5.184643 5.038033 5.030633 5.194101 1114_at 7.626418 7.667100 7.485715 7.527473 1115_at 5.205119 5.266216 5.178946 4.894278 1116_at 8.008179 8.000449 7.952617 7.740922 1117_at 7.404985 7.340807 7.343723 7.647608 1118_at 6.249478 6.276219 6.089551 6.149665 1119_at 8.505232 8.371515 8.932111 8.904370 112_g_at 5.842315 5.917530 5.667464 5.660869 1120_at 9.767162 9.700040 9.547721 9.385500 1121_g_at 8.772440 8.822221 8.552295 8.578667 1122_f_at 9.289137 9.385932 9.310750 9.464966 1123_at 7.856048 7.860670 7.661996 7.704481 1124_at 8.819600 8.790563 8.733143 8.637403 1125_s_at 6.190725 6.154517 6.919367 6.978009 1126_s_at 6.345293 6.158996 8.038418 8.031522 1127_at 9.509133 9.479713 9.416069 9.408498 1128_s_at 7.094273 7.254396 7.115945 7.120836 1129_at 6.191378 6.461422 6.475375 6.664051 113_i_at 6.607461 6.429772 6.988697 6.804289 1130_at 8.863632 8.796711 8.803089 8.702122 1131_at 10.440073 10.261516 10.285989 10.284372 1132_s_at 8.271977 8.371165 8.032393 8.182505 1133_at 6.585692 6.479490 6.513345 6.587153 1134_at 8.945401 8.894785 8.871334 8.879432 1135_at 6.169868 6.259425 6.264439 6.217580 1136_at 8.076560 8.146176 8.752608 8.761179 1137_at 6.247532 6.128254 6.096088 5.688080 1138_at 9.347829 9.340181 9.742051 9.566695 1139_at 7.321429 7.470596 7.594528 7.595004 114_r_at 6.752378 6.996440 6.819265 7.300634 1140_at 6.217907 6.246775 6.758112 6.440181 1141_at 6.414573 6.456191 6.313663 6.345891 1142_at 7.461140 7.760287 7.639871 7.500065 1143_s_at 7.020785 6.790222 6.716995 6.796487 1144_at 5.664689 5.657590 5.597171 5.478647 1145_g_at 7.478242 7.294096 6.961118 7.399034 1146_at 6.459534 6.606949 6.494189 6.482466 1147_at 4.384986 4.808472 4.803987 4.646416 1148_s_at 5.473025 5.455870 5.310022 5.419198 1149_at 5.913087 6.016720 5.917721 6.123515 115_at 8.722841 8.668305 9.225390 9.542206 1150_at 5.498177 5.723247 5.658636 5.581356 1151_at 10.892914 10.789973 10.858475 10.826333 1152_i_at 5.183936 5.390605 5.114804 6.929243 1153_f_at 9.801283 9.921274 9.737189 9.749568 1154_at 9.092248 9.058277 9.687039 9.633673 1155_at 7.660476 7.730831 7.620944 7.585311 1156_at 7.149759 7.388900 7.156863 7.376540 1157_s_at 5.330659 5.559739 5.670561 5.357460 1158_s_at 10.112277 9.983527 10.057355 10.370670 1159_at 4.629963 4.708841 4.566159 4.725699 116_at 5.737638 6.089805 5.981398 6.183673 1160_at 10.791386 10.757484 11.168153 11.115442 1161_at 12.667830 12.579313 12.963441 13.045040 1162_g_at 8.536611 8.441872 8.396606 8.524592 1163_at 6.660581 6.450130 6.727868 6.360846 1164_at 6.038261 6.123203 5.790907 5.841051 1165_at 4.694700 4.823361 4.669727 4.514121 1166_at 10.467059 10.433619 10.750785 10.723815 1167_s_at 9.178905 9.456310 9.214573 9.208117 1168_at 5.861177 5.941523 5.851579 5.968628 1169_at 6.787779 7.089235 6.753190 7.327670 117_at 6.940412 6.819932 6.789709 7.041181 1170_at 6.159156 6.249633 6.225018 6.311019 1171_s_at 7.497643 7.281123 7.284395 7.232310 1172_at 6.910771 7.332442 6.979994 6.958571 1173_g_at 9.039339 9.102146 8.856890 8.530897 1174_at 5.782953 5.913419 5.818924 5.978057 1175_s_at 5.909708 5.891830 5.951577 5.885654 1176_at 6.053897 6.160595 6.242513 6.121749 1177_at 7.616002 7.660142 7.553390 7.177500 1178_at 4.937006 5.019617 6.317796 6.014079 1179_at 11.672312 11.659940 12.486494 12.478607 118_at 6.601571 6.697817 6.661748 6.585518 1180_g_at 12.435150 12.450849 13.130448 13.122134 1181_at 8.176006 8.217209 8.258458 8.389053 1182_at 4.725474 4.816837 4.937953 4.811216 1183_at 5.488699 5.705196 5.407262 5.892592 1184_at 10.322797 10.253449 10.489564 10.360903 1185_at 7.924885 8.028490 8.009776 8.134265 1186_at 5.038839 5.050179 4.939852 4.993458 1187_at 8.192555 8.280466 8.163043 8.292743 1188_g_at 7.169269 7.189823 7.241881 7.244818 1189_at 8.209994 8.101179 8.055505 8.436116 1190_at 4.755343 4.969887 4.892919 5.148720 1191_s_at 9.126640 9.168386 9.565245 9.291001 1192_at 8.267728 8.072924 8.487194 8.333200 1193_at 7.508511 7.774522 7.755693 7.817416 1194_g_at 6.152872 6.271768 6.391836 6.266732 1195_s_at 5.209147 5.092169 5.441336 5.350013 1196_at 9.746420 9.871883 9.807166 9.919873 1197_at 9.022706 8.798213 9.062429 8.929801 1198_at 4.779926 4.668907 4.654630 4.468582 1199_at 11.933571 11.911517 12.168298 12.114986 120_at 5.299022 5.407787 5.440184 5.236345 1200_at 6.520670 6.761889 6.701188 6.840567 1201_at 5.675533 5.790996 5.579206 5.656774 1202_g_at 6.505906 6.617518 6.478991 6.247579 1203_at 5.423680 5.404976 5.385306 5.469026 1204_at 5.337570 5.603316 5.421783 5.434357 1205_at 5.349139 5.561175 5.530734 5.647664 1206_at 8.754972 8.844281 8.653677 8.504147 1207_at 5.805534 5.929592 5.744153 5.521579 1208_at 8.271127 8.175548 8.195207 8.367326 1209_at 6.143915 6.333781 6.165712 5.904267 121_at 9.604369 9.671733 9.620272 9.580364 1210_s_at 8.313796 8.454149 8.205983 8.341861 1211_s_at 7.242683 7.360323 7.063163 6.668509 1212_at 9.902969 10.038373 9.902967 9.869500 1213_at 6.529330 6.368777 6.212938 5.802598 1214_s_at 4.792867 4.843260 4.826859 4.979163 1217_g_at 5.354328 5.376136 5.275101 5.872149 1218_at 9.030393 8.992841 9.210727 9.145547 1219_at 7.789200 7.680699 7.621431 7.510299 122_at 6.554707 6.767977 6.997614 6.879143 1220_g_at 8.100243 8.012898 7.744230 7.860193 1221_at 7.900538 8.089284 7.543237 7.845957 1222_at 5.414985 5.266025 5.188459 5.204643 1223_at 7.939047 7.886436 7.662560 7.894346 1224_at 8.971380 8.731318 8.686488 8.659580 1225_g_at 9.524663 9.457605 9.374483 9.319558 1226_at 5.660812 5.526849 5.468480 5.914177 1227_g_at 6.289310 6.275589 6.027628 6.439628 1228_s_at 7.867547 7.877714 7.718126 7.587791 1229_at 6.807557 6.834646 6.990954 6.575523 123_at 5.366212 5.289484 5.354638 5.479024 1230_g_at 7.859280 7.866079 7.882202 7.690612 1231_at 5.462948 5.337994 5.032186 4.827131 1232_s_at 5.000169 5.374661 4.943377 4.827683 1233_s_at 9.645794 9.791881 9.666370 9.775713 1234_at 5.680978 6.041152 5.784085 5.734383 1235_at 12.906955 12.733674 12.685621 12.885845 1236_s_at 6.408729 6.362832 6.285292 6.364081 1237_at 10.231875 10.099423 10.417377 10.445325 1238_at 9.372374 9.382203 9.591486 9.443424 1239_s_at 6.195267 6.345840 6.275786 6.486315 1240_at 7.165026 7.328330 7.333109 7.342521 1241_at 9.932252 10.072237 10.924494 10.756663 1242_at 10.200452 10.129296 9.851558 9.839039 1243_at 8.761777 8.774014 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901_g_at 4.741662 4.783829 4.593532 4.716454 902_at 5.489113 5.408025 5.509220 5.628394 903_at 7.641855 7.594029 8.474308 8.167256 904_s_at 4.884100 5.006747 6.760628 6.285376 905_at 11.028057 10.879996 10.913910 10.638403 906_at 5.897992 6.077626 5.944786 6.051995 907_at 6.633679 6.504252 6.534171 6.591042 908_at 7.098634 7.041896 6.808532 6.687127 909_g_at 6.351384 6.273929 5.940005 5.944646 910_at 7.397465 7.104903 11.121519 11.090972 911_s_at 11.585149 11.051634 12.016069 11.605751 912_s_at 6.476998 6.239221 6.719174 6.804193 913_at 6.232099 5.983218 5.565164 6.015134 914_g_at 4.887528 4.739292 4.797757 4.790608 915_at 10.129980 9.628146 9.217263 8.595912 916_at 9.477532 9.371643 9.420344 9.697348 917_g_at 8.696949 8.821848 8.347948 8.876337 918_at 9.110363 8.797615 8.453013 8.804382 919_at 7.604085 7.651562 7.166575 7.641249 920_at 6.525900 6.644513 6.055423 6.222531 921_s_at 7.438261 7.475906 7.128534 7.359146 922_at 11.895924 11.644547 11.929511 11.616169 923_at 7.632842 7.981158 7.147059 7.760304 924_s_at 8.716085 8.537921 8.466814 7.806509 925_at 11.311580 11.069988 11.060390 10.803617 926_at 6.808592 6.548578 6.641858 6.799613 927_s_at 9.383251 9.496684 8.974799 9.198576 928_at 4.642361 4.682155 4.663831 4.623556 929_at 5.684569 5.923105 5.408906 5.758704 930_at 5.647402 5.420215 5.376915 5.361186 931_at 4.790547 4.742989 4.651149 4.720757 932_i_at 9.237122 9.034619 8.969052 8.895354 933_f_at 7.829260 7.673829 7.489094 7.510012 934_at 6.134276 6.096011 6.177740 6.470645 935_at 10.248977 9.767219 9.913852 9.364376 936_s_at 6.652819 6.531761 6.421830 6.663791 937_at 8.407613 8.412293 8.086954 8.582361 [ reached getOption("max.print") -- omitted 126 rows ] 
eset_mas5<-mas5(affybatch.estrogen)
background correction: mas PM/MM correction : mas expression values: mas background correcting...done. 12625 ids to be processed | | |####################| 
e_mas5<-exprs(eset_mas5)
show(e_mas5)
low10-1.cel low10-2.cel high10-1.cel high10-2.cel 100_g_at 8.841852e+02 1.211845e+03 7.125318e+02 6.467652e+02 1000_at 3.187346e+03 2.724568e+03 2.072193e+03 2.120803e+03 1001_at 3.970776e+01 1.818771e+01 1.589701e+01 5.329840e+01 1002_f_at 2.205818e+01 3.921241e+01 1.383366e+01 2.047484e+01 1003_s_at 5.799479e+01 6.084516e+01 1.856003e+02 1.938242e+02 1004_at 1.525780e+02 1.635449e+02 1.698508e+02 1.612442e+02 1005_at 7.050029e+02 7.662848e+02 3.137365e+02 4.059544e+02 1006_at 2.120307e+01 4.188329e+00 2.048994e+01 2.262188e+01 1007_s_at 8.383247e+03 7.866760e+03 5.261891e+03 6.496665e+03 1008_f_at 1.634609e+03 5.124613e+03 4.198788e+03 9.226769e+02 1009_at 2.966029e+03 2.789746e+03 4.598059e+03 4.052111e+03 101_at 2.324743e+01 1.541839e+01 1.722251e+01 1.534156e+01 1010_at 1.736519e+01 3.968644e+01 1.746486e+01 6.121554e+01 1011_s_at 7.328722e+02 8.564684e+02 9.071976e+02 7.672434e+02 1012_at 8.348870e+01 7.749091e+01 7.072225e+01 6.215320e+01 1013_at 1.147546e+02 7.901453e+01 1.137053e+02 1.167283e+02 1014_at 1.080620e+03 1.143464e+03 1.084494e+03 7.657347e+02 1015_s_at 5.244243e+01 1.462038e+02 4.645188e+01 2.498275e+01 1016_s_at 1.358892e+01 4.667975e+01 5.210842e+01 3.336456e+01 1017_at 8.914314e+01 8.827552e+01 9.396083e+01 8.171480e+01 1018_at 6.185392e+01 8.898151e+01 8.793711e+01 7.641729e+01 1019_g_at 2.432797e+02 2.872168e+02 2.175104e+02 2.304868e+02 102_at 6.105234e+01 5.614400e+01 3.899282e+01 3.924108e+01 1020_s_at 3.209820e+03 3.336758e+03 2.184607e+03 2.755012e+03 1021_at 8.751481e+01 4.620445e+01 3.913030e+01 2.557162e+01 1022_f_at 4.518682e+01 2.155817e+01 3.317248e+01 5.270055e+01 1023_at 2.378648e+01 2.015079e+01 3.710382e+01 3.606208e+01 1024_at 5.840660e+02 6.987656e+02 1.773468e+02 2.933188e+02 1025_g_at 5.096002e+02 5.747120e+02 1.988394e+02 2.966254e+02 1026_s_at 6.946996e+01 1.361604e+02 2.140055e+02 1.103340e+02 1027_at 5.866248e+01 1.478940e+01 1.713642e+01 1.078330e+02 1028_at 2.184483e+02 2.154131e+02 3.394950e+02 1.634929e+02 1029_s_at 2.395127e+01 3.984020e+01 1.643578e+01 2.110383e+01 103_at 1.190715e+02 6.110296e+01 9.484485e+01 8.662103e+01 1030_s_at 3.422685e+03 3.126352e+03 2.740896e+03 3.067077e+03 1031_at 1.826463e+02 2.218934e+02 2.341170e+02 3.618271e+02 1032_at 3.945400e+02 3.064313e+02 2.730041e+02 3.884783e+02 1033_g_at 9.798672e+01 6.364647e+01 1.214681e+02 4.134730e+01 1034_at 1.164267e+03 1.098165e+03 6.099554e+02 6.703792e+02 1035_g_at 1.040412e+03 1.137425e+03 7.673596e+02 8.381568e+02 1036_at 1.187226e+01 2.494394e+00 2.398896e+00 1.657206e+01 1037_at 9.931331e+01 4.699798e+01 3.347178e+01 5.758020e+01 1038_s_at 1.625577e+02 1.892190e+02 1.636234e+02 1.368300e+02 1039_s_at 3.290409e+02 2.258241e+02 3.130187e+02 3.212982e+02 104_at 9.077338e+01 9.776274e+01 1.299096e+02 9.673623e+01 1040_s_at 6.539164e+01 7.341299e+01 8.234662e+01 8.462000e+01 1041_at 8.520395e+01 1.074632e+02 8.617436e+01 8.223033e+01 1042_at 2.479347e+01 3.345793e+01 1.863503e+01 7.414258e+00 1043_s_at 4.350524e+01 1.349898e+01 3.638942e+01 1.551443e+01 1044_s_at 4.037298e+02 4.109983e+02 2.528050e+02 2.499125e+02 1045_s_at 4.342571e+02 3.959472e+02 3.149589e+02 3.185372e+02 1046_at 3.918729e+02 3.607047e+02 2.386337e+02 2.726072e+02 1047_s_at 1.522358e+02 2.276217e+02 1.151285e+02 1.357836e+02 1048_at 7.018503e+01 7.143450e+01 5.743519e+01 9.421463e+01 1049_g_at 4.566575e+01 5.058378e+01 3.046743e+01 4.517276e+01 105_at 8.031170e+00 3.195534e+00 6.129577e+00 1.195762e+01 1050_at 3.883570e+00 6.183381e+00 3.239136e+00 2.162512e+00 1051_g_at 9.649552e+01 9.745076e+01 7.449195e+01 3.027303e+01 1052_s_at 9.705532e+02 1.157240e+03 6.484940e+02 5.399729e+02 1053_at 2.166325e+02 2.944247e+02 5.421804e+02 4.620013e+02 1054_at 4.899094e+01 5.303629e+01 2.030391e+02 2.770662e+02 1055_g_at 6.232443e+01 1.215561e+02 7.123164e+02 5.558385e+02 1056_s_at 9.400789e+01 1.710141e+01 1.233742e+01 4.410916e+01 1057_at 6.481072e+03 6.730464e+03 3.451371e+03 3.461748e+03 1058_at 2.945722e+02 1.500433e+02 2.802133e+02 2.469610e+02 1059_at 1.196336e+01 4.232848e+01 3.343548e+01 7.895841e+00 106_at 1.500140e+01 8.399834e+00 1.320759e+01 1.370135e+01 1060_g_at 9.271116e+01 7.377200e+01 1.006193e+02 1.412020e+02 1061_at 3.982883e+01 7.532953e+01 3.772735e+01 7.726194e+01 1062_g_at 4.237013e+01 1.063823e+01 3.729868e+01 1.599259e+01 1063_s_at 5.846979e+02 4.611842e+02 3.942131e+02 4.115153e+02 1064_at 3.065191e+02 2.358853e+02 2.734780e+02 2.901774e+02 1065_at 2.474112e+01 4.604097e+01 8.694690e+01 2.605109e+01 1066_at 1.748137e+02 1.156233e+02 9.274444e+01 1.546571e+02 1067_at 5.649961e+01 4.423499e+01 4.977069e+00 1.107962e+01 1068_g_at 8.044711e+01 7.335343e+01 6.858648e+01 9.312279e+01 1069_at 2.880735e+01 4.145216e+00 4.868848e+00 6.460091e+01 107_at 1.005328e+02 5.216157e+01 6.193848e+01 3.186537e+01 1070_at 1.091790e+02 1.524724e+02 1.208434e+02 1.911455e+02 1071_at 2.940870e+02 2.977044e+02 2.629609e+02 6.823203e+01 1072_g_at 6.810160e+02 6.479906e+02 4.795030e+02 4.003868e+02 1073_at 1.219729e+03 9.103185e+02 1.297677e+03 1.489313e+03 1074_at 8.723429e+02 6.831097e+02 8.010589e+02 8.065705e+02 1075_f_at 6.058510e+01 7.087058e+01 1.471703e+01 6.331799e+01 1076_at 1.155312e+02 1.326590e+02 5.882287e+01 1.205493e+02 1077_at 1.468823e+01 4.321758e+00 6.208728e+00 3.542881e+01 1078_at 3.063714e+02 2.018487e+02 2.556562e+02 3.603923e+02 1079_g_at 6.526697e+02 9.375424e+02 6.863825e+02 8.697758e+02 108_g_at 3.337657e+02 4.856263e+02 3.976689e+02 3.822667e+02 1080_s_at 1.161397e+01 9.776999e+00 4.347016e+00 1.501681e+01 1081_at 3.048955e+03 3.170949e+03 2.604710e+03 2.894083e+03 1082_at 1.805687e+02 1.570211e+02 1.794516e+02 1.782903e+02 1083_s_at 2.532701e+02 2.935711e+02 1.806079e+02 1.946688e+02 1084_at 2.642520e+01 5.099001e+01 2.305998e+01 1.693567e+01 1085_s_at 3.717866e+02 4.693641e+02 3.026832e+02 3.114335e+02 1086_at 1.273532e+01 4.141058e+01 1.290466e+01 2.864974e+01 1087_at 4.710944e+02 4.789171e+02 7.190102e+01 4.887621e+01 1088_at 7.694293e+00 1.079089e+01 3.287697e+01 3.660926e+01 1089_i_at 1.662617e+01 2.056823e+01 2.098623e+02 6.527096e+02 109_at 5.849466e+02 6.440202e+02 5.595716e+02 5.855755e+02 1090_f_at 9.422401e+00 5.769136e+01 9.651067e+01 3.530348e+01 1091_at 1.689757e+03 1.737900e+03 1.536961e+03 1.547222e+03 1092_at 4.045578e+02 8.171818e+02 7.013135e+02 7.744662e+02 1093_at 2.547880e+01 6.897456e+01 6.932395e+01 8.946450e+01 1094_g_at 1.630712e+02 1.818371e+02 2.130544e+02 2.428730e+02 1095_s_at 3.337813e+00 2.784096e+01 2.007041e+01 2.423472e+01 1096_g_at 1.547355e+02 1.148412e+02 3.444790e+01 2.163977e+02 1097_s_at 1.428244e+02 1.721742e+02 1.271145e+02 1.806160e+02 1098_at 1.206888e+01 7.025118e+00 1.952721e+00 3.060501e+01 1099_s_at 2.997358e+01 3.458297e+01 7.980432e+01 3.415482e+01 110_at 1.370647e+02 1.446642e+02 9.936338e+01 9.290322e+01 1100_at 2.039108e+03 1.689768e+03 2.684093e+03 2.942693e+03 1101_at 3.285714e+01 9.783321e+00 2.307822e+01 2.874402e+01 1102_s_at 2.603107e+02 2.380059e+02 1.545810e+02 1.754976e+02 1103_at 6.111539e+00 1.334961e+01 3.181089e+01 1.204107e+01 1104_s_at 4.337635e+03 4.476203e+03 3.121235e+03 3.336834e+03 1105_s_at 3.240574e+02 5.624205e+02 3.989156e+02 4.509298e+02 1106_s_at 1.361830e+02 2.298968e+02 2.600820e+01 2.342288e+01 1107_s_at 2.584313e+04 2.778663e+04 2.172344e+04 1.805772e+04 1108_s_at 2.502915e+02 1.868428e+02 9.844196e+01 2.455089e+02 1109_s_at 4.437323e+02 5.646860e+02 2.209784e+02 2.142535e+02 111_at 8.381247e+02 1.054058e+03 6.763981e+02 6.963725e+02 1110_at 1.279485e+02 1.273500e+02 8.102658e+01 7.445469e+01 1111_at 1.350275e+01 3.479024e+01 1.135010e+01 5.457323e+01 1112_g_at 9.920336e+01 1.069625e+02 2.761315e+01 1.332242e+02 1113_at 4.813707e+00 6.702112e+00 1.131052e+01 1.185466e+01 1114_at 1.588168e+02 2.515607e+02 1.472618e+02 2.235930e+01 1115_at 4.835482e+01 6.689063e+01 6.357261e+01 2.397644e+01 1116_at 2.588656e+02 2.756685e+02 2.587349e+02 2.244581e+02 1117_at 8.457366e+01 1.080796e+02 1.131937e+02 1.689957e+02 1118_at 1.214412e+02 1.362380e+02 1.235214e+02 1.901771e+02 1119_at 7.212718e+02 5.922943e+02 1.075623e+03 1.152028e+03 112_g_at 1.272893e+02 1.488054e+02 6.020925e+01 1.327244e+02 1120_at 1.187263e+03 1.211014e+03 1.113254e+03 1.129071e+03 1121_g_at 7.158799e+02 6.865181e+02 7.012552e+02 7.380020e+02 1122_f_at 5.344462e+02 5.667175e+02 4.594348e+02 5.306355e+02 1123_at 7.306597e+01 2.984513e+01 2.570350e+01 5.280842e+01 1124_at 8.322704e+02 8.770885e+02 6.962726e+02 6.017310e+02 1125_s_at 1.265118e+02 9.488155e+01 3.068912e+02 3.696628e+02 1126_s_at 1.647365e+02 1.496338e+02 6.732051e+02 7.142816e+02 1127_at 9.493163e+02 8.497371e+02 9.021588e+02 8.071625e+02 1128_s_at 4.693636e+01 1.748088e+02 6.457709e+01 1.942896e+02 1129_at 1.491835e+01 2.644323e+01 1.461412e+01 2.427483e+01 113_i_at 7.149960e+01 1.526136e+02 1.794357e+02 1.690129e+02 1130_at 7.954740e+02 8.043914e+02 7.279335e+02 8.386385e+02 1131_at 1.428371e+03 1.433875e+03 1.291682e+03 1.625331e+03 1132_s_at 5.063165e+02 4.078305e+02 2.594414e+02 3.191709e+02 1133_at 2.952859e+01 2.012233e+01 4.099701e+01 1.316411e+01 1134_at 7.538767e+02 7.650158e+02 7.046587e+02 7.647243e+02 1135_at 3.853956e+01 1.487832e+02 1.289167e+02 5.026531e+01 1136_at 4.772380e+02 5.344043e+02 9.234397e+02 1.508837e+03 1137_at 1.323137e+02 1.060754e+02 8.157675e+01 1.741525e+02 1138_at 1.312520e+03 1.376975e+03 1.561562e+03 1.925831e+03 1139_at 3.298953e+02 3.216900e+02 3.650077e+02 4.994742e+02 114_r_at 8.523452e+00 1.308838e+01 7.806780e+00 1.409880e+01 1140_at 1.699470e+02 1.378948e+02 2.854864e+02 3.065556e+02 1141_at 1.557211e+02 1.574419e+02 1.298924e+02 1.896558e+02 1142_at 2.142284e+02 3.151865e+02 2.550867e+02 2.090112e+02 1143_s_at 2.140999e+02 1.780449e+02 8.849297e+01 1.265875e+02 1144_at 5.078481e+01 3.629485e+01 1.557206e+01 2.030980e+01 1145_g_at 2.048090e+02 5.566192e+01 6.791396e+01 4.146434e+01 1146_at 2.991652e+01 3.430814e+01 5.136073e+01 1.474425e+01 1147_at 4.858544e+00 4.339037e+01 4.741573e+01 1.521212e+01 1148_s_at 4.176132e+01 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669.039041 919_at 336.457305 318.864450 138.729125 324.277137 920_at 272.272185 244.303593 54.831370 112.489395 921_s_at 102.697917 131.090014 42.839636 80.424955 922_at 9450.134462 8416.709947 8423.250280 7944.466973 923_at 187.536910 292.638960 43.387125 206.188902 924_s_at 873.331690 850.296676 621.816064 785.403223 925_at 7946.476535 5227.635684 6117.528729 4324.432120 926_at 176.530906 111.211701 37.384433 97.557050 927_s_at 1282.233226 1469.689815 590.650273 755.084883 928_at 14.284425 9.609085 14.098079 17.405361 929_at 139.266275 176.536015 52.657832 120.899994 930_at 168.949262 103.378712 19.548195 86.140713 931_at 40.500761 73.785508 3.329233 4.587939 932_i_at 1447.133488 1427.771029 925.286508 1111.109334 933_f_at 577.076277 485.897442 329.759696 499.657608 934_at 144.486961 163.449180 131.697723 291.141290 935_at 2936.727473 2373.598250 2149.005531 1724.773315 936_s_at 60.951520 32.852098 20.665297 25.072033 937_at 41.359260 88.879072 35.540504 110.169610 [ reached getOption("max.print") -- omitted 126 rows ] 
par(mfrow=c(1,2))
d1<-density(e_rma)
plot(d1)
d2<-density(e_mas5)
plot(d2)
Image in a Jupyter notebook
par(mfrow=c(1,2))
boxplot(e_rma)
boxplot(e_mas5)
Image in a Jupyter notebook
log2e_mas5<-log2(e_mas5)
show(log2e_mas5)
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7.7850579 8.0530464 7.5759554 7.8850994 726_f_at 8.5233974 8.2401525 8.4405094 8.3379816 727_at 9.4948512 9.0653847 8.3115417 9.4943134 728_at 4.5519125 6.1901937 4.2176541 6.9835184 729_i_at 9.4961458 9.5934796 8.7612910 9.3741251 730_r_at 8.6363726 9.5459135 8.5526499 9.2554442 731_f_at 7.8850404 8.7188495 6.8076976 8.6720646 732_f_at 7.6720228 8.3825945 7.3250789 8.2970317 733_at 7.4627679 3.7748545 4.2568245 2.8336205 734_at 8.5321342 8.8934361 8.2834278 7.2751918 735_s_at 7.8473094 7.3926976 6.4874114 7.8209104 736_f_at 7.8779700 8.2068169 8.1880737 8.6808785 737_at 4.8113822 5.0629056 3.7141706 4.9950592 738_at 7.3320545 7.4586690 7.9599556 7.5238975 739_at 6.5635861 3.3369911 6.5892704 4.6577480 740_at 7.7978051 7.4944500 6.7782601 7.5019738 741_g_at 3.2945223 4.8933984 3.1581139 4.6536246 742_at 5.0916871 6.1040916 4.3007871 5.0950296 743_at 6.3913136 2.6327006 2.4873025 3.0699651 744_at 7.5163857 5.4996142 7.3299339 7.8955697 745_at 10.6665448 10.4002434 9.7181665 10.1648554 746_at 6.0993199 3.9254643 3.2711528 7.3462425 747_at 5.3704268 5.7553464 4.5498758 5.2339752 748_s_at 6.2583360 6.1586465 6.7676856 7.5970474 749_at 8.9828168 9.0797270 10.1101235 10.3474895 750_at 6.0622062 6.5951479 5.4024703 5.4604277 751_at 10.4041726 9.5117505 10.0926843 10.3415957 752_s_at 11.5235079 11.5238266 11.2178115 10.9219978 753_at 6.1840239 4.3071306 5.3822719 5.1631655 754_s_at 10.3438364 9.7057706 10.0588724 10.0555787 755_at 7.2383330 7.2330992 7.3468538 6.5807746 756_at 5.9845883 6.3191699 1.8891533 5.8893422 757_at 10.9085894 11.1499754 8.6211325 9.2655621 758_at 5.5640625 6.0821940 6.7981531 6.7347908 759_at 4.9099612 4.1672065 4.2782755 6.7211099 760_at 8.6076562 8.8629877 8.3033959 7.7644763 761_g_at 8.1663646 7.6810538 7.8667538 8.3849795 762_f_at 9.7720524 9.6664974 9.0456869 9.4287992 763_at 9.1833772 9.1651549 9.1582062 8.9922706 764_s_at 3.7633205 4.2826218 4.8482731 4.2622967 765_s_at 5.2952952 4.3794897 4.3455630 4.9548853 766_at 9.3420208 9.5708776 8.8628267 9.7158535 767_at 7.0576859 7.6449145 4.4243712 7.4618025 768_at 6.3084881 4.0704145 6.8744479 5.7136972 769_s_at 14.8586298 15.0640487 13.5444377 13.3341149 770_at 8.3982787 8.5329489 8.5135084 8.8772006 771_s_at 6.4835362 8.4444272 8.3079015 8.5913164 772_at 8.2087413 8.1537530 7.6009337 8.1905585 773_at 4.5485883 4.3314041 1.8302847 4.3008459 774_g_at 6.9527859 3.2584520 1.9958040 4.1013981 775_at 5.5435632 4.9630137 6.8706762 7.4852426 776_at 8.5672431 8.8290351 9.3996671 9.3135868 777_at 10.8742675 10.9525402 10.3158188 11.3094968 778_s_at 8.9659708 8.8028828 8.8912857 8.6361617 779_at 3.8888829 4.2380933 3.3617909 3.3582570 780_at 7.4092721 8.1700463 7.0938495 6.0952226 781_at 8.3300670 8.1358938 9.0543399 8.4927817 782_at 9.0038991 8.4367016 8.9983873 8.4952912 783_at 9.8998283 9.6412346 9.3406705 9.4882873 784_g_at 9.6755053 9.1776114 8.6335477 8.6337552 785_at 8.7727560 7.6375811 8.1260246 8.2955007 786_at 7.0661055 7.4463439 8.5502943 8.4659972 789_at 8.8699665 9.6164042 7.6838470 8.3045172 790_at 5.4138262 4.9736895 6.1061204 6.2563147 791_g_at 5.1574637 5.4667743 6.1380761 5.1780404 792_s_at 9.8325424 10.1585690 7.4489128 9.9149281 793_at 7.5662611 8.8302198 7.8358359 8.3441122 794_at 8.7847865 8.3984677 8.4262589 8.3545356 795_s_at 5.9231490 4.3856598 6.1979304 6.2755399 796_i_at 3.6759378 2.9567642 5.6273100 3.1071178 797_at 3.7452405 3.4701799 3.8312845 3.6654480 798_at 7.5014112 6.6777064 8.8626212 8.4711692 799_at 9.0195840 9.5061970 9.2259069 9.5211650 800_g_at 6.2257549 6.8280624 5.7139706 8.7013423 801_at 7.1853385 6.7862575 4.5552254 4.6446677 802_at 8.3448159 8.1865404 7.8763816 8.0649747 803_at 3.7323678 3.4845653 5.2767707 3.2202546 804_s_at 6.7993313 7.3334541 7.3237468 7.0570902 805_at 4.0069244 5.2841033 4.6768770 4.9603533 806_at 10.0845297 10.8582274 9.6091218 10.2675421 807_at 7.4061866 6.0789148 6.2761791 6.8709417 808_at 5.6209948 5.2745518 2.9662239 3.8774061 809_at 7.1171810 6.5919050 7.1627779 7.6379428 810_at 9.3708522 9.3759818 8.9285440 9.3868555 811_at 10.4271499 10.1753949 11.4032319 10.4494499 812_at 8.3499713 8.3407330 7.5930233 8.1158368 813_at 3.0381562 5.7940800 2.2953022 3.4300404 814_s_at 1.9779800 3.1630570 3.3819249 5.6730561 815_at 5.5332184 6.0528840 7.7688147 6.4451625 816_g_at 9.2001732 8.9821788 9.8730399 10.0359938 817_at 7.1210813 6.0661365 6.3865792 7.4189277 818_s_at 8.0899059 7.3723378 8.0312741 7.4222562 819_at 3.0137440 3.2905272 3.4304599 3.4867139 820_at 8.4195157 6.7831521 9.2933053 9.1224855 821_s_at 5.3439975 5.2356170 3.8913432 7.5928192 822_s_at 7.7970295 8.5933989 7.9105070 8.7675650 823_at 5.1437899 7.8028129 6.0541415 6.5045914 824_at 9.8913508 10.1598838 10.9397278 10.8180516 825_at 6.7090310 4.5400729 3.7710287 6.5020012 826_at 8.3446320 7.9865268 7.3380861 8.3959314 827_s_at 4.7713704 5.1125059 4.6703654 4.6084271 828_at 3.5196569 4.4918057 5.4638356 4.4167082 829_s_at 8.0701810 7.7830729 7.4062031 9.1441989 830_at 7.5077211 5.7109263 5.0982747 8.7952316 831_at 7.3226576 7.1797782 8.0446172 8.2082491 832_at 10.2880890 10.7348685 10.1938565 10.8615556 833_at 6.1641365 6.6971286 7.0977926 7.3833595 834_at 7.1752542 7.6482380 6.1615871 5.6672924 835_at 10.0152866 9.2624249 9.7577982 10.0041120 836_at 4.8905756 6.7900107 5.1698972 7.4740821 837_s_at 8.4678484 7.7231888 8.4673305 8.1587012 838_s_at 12.8325992 12.7612490 12.8714411 12.9789927 839_at 2.6409447 4.8393507 2.5441297 1.9711620 840_at 8.9409776 8.2985304 9.0655200 8.4888430 841_at 2.8444368 6.3469975 3.6438840 5.6587001 842_at 8.9601349 8.3695222 8.7580696 8.8463681 843_at 8.5811886 8.3999646 8.9337815 8.7618459 844_at 8.2073584 8.5955325 6.5482150 6.0371757 845_at 7.7791853 6.6810350 7.4501960 7.6528565 846_s_at 10.9821844 10.8750641 7.6986904 7.3356823 847_at 8.3790006 8.3833881 8.7488344 8.0640364 848_at 8.3271833 6.8746278 6.6440056 6.9236003 849_g_at 7.0742038 7.6638971 6.1214216 5.5054257 850_r_at 6.8530510 7.1746154 5.4130469 6.9349876 851_s_at 8.4991886 8.1316984 9.0880940 8.9573976 852_at 6.3476049 4.1945205 5.8224832 6.2964173 853_at 8.9713363 9.0359532 8.6585201 8.6330797 854_at 5.8956332 8.4230908 5.9843144 6.9903541 855_at 9.3015790 9.3110196 9.0462106 8.9030327 856_at 6.5772004 5.7975392 5.2828139 6.9602941 857_at 7.8155009 8.1339540 7.4628167 7.8816109 858_at 10.6233437 10.4947679 10.4353121 10.3855381 859_at 8.4093316 8.0922202 7.9670182 8.1111521 860_at 7.7117070 8.2031539 9.7336858 8.8735013 861_g_at 7.1096404 7.6354151 8.0568069 8.0535595 862_at 3.5809240 5.1148183 7.0454290 7.1616793 863_g_at 6.7750150 3.4031565 6.1805434 5.8723396 864_at 8.1738268 8.5262729 8.4519547 8.2124435 865_at 8.2240828 7.5452308 7.5354598 8.3431882 866_at 7.1578154 8.3409851 6.9041755 7.0448647 867_s_at 9.5943448 9.1960589 6.0553882 9.5935997 868_at 10.6853055 10.4816074 10.5832355 9.8689040 869_at 9.6622246 9.1224016 9.6962340 9.8450073 870_f_at 10.1771431 10.4951315 10.5165818 11.3181820 871_s_at 5.7314828 4.7681015 5.7398415 6.6778305 872_i_at 7.1261674 7.7951870 7.8209203 7.8778766 873_at 2.9616305 3.1520881 6.9958326 3.8912596 874_at 7.1176970 7.5919018 5.5237721 4.9647683 875_g_at 4.9741621 7.3413355 5.6862077 5.7398000 876_at 5.6353838 6.0073250 5.6697757 6.4916533 877_at 6.9980953 5.2029059 6.7232476 7.1853947 878_s_at 6.4991709 6.2372649 5.9669323 6.8264381 879_at 7.7755841 7.9863526 6.7225039 7.3437550 880_at 11.8281724 11.6825915 11.9047315 11.6410572 881_at 9.4233151 9.1359199 4.6083602 5.6893324 882_at 11.9152127 12.2540929 11.7005343 12.0379191 883_s_at 9.3390342 8.8172967 9.4044158 9.8025893 884_at 11.0739301 11.2456031 10.2301576 10.6047145 885_g_at 9.8367781 10.1425965 8.1478353 8.4246419 886_at 6.1435351 6.8145026 5.9236847 5.8512984 887_at 10.1258116 9.6974438 9.6108921 10.0394892 888_s_at 9.3580709 8.5912751 8.6969806 9.1570145 889_at 6.3124625 3.5303647 4.9948488 5.7362785 890_at 8.9777527 9.0548947 9.2335915 8.9385475 891_at 8.8261883 8.6016745 9.0300630 9.0560695 892_at 8.1363188 8.5869473 5.5366343 3.7565215 893_at 11.0239288 10.7331557 12.5808276 12.6765656 894_g_at 11.9012161 11.0695309 12.7922018 13.0562242 895_at 14.5698469 14.5881518 14.6588632 14.9529203 896_at 5.9826845 5.4784680 6.9517455 7.0403060 897_at 10.2855335 10.0505815 9.8611835 10.0968086 898_s_at 8.4966746 9.1582947 8.0488776 9.2651705 899_at 5.9409092 8.2053638 6.5532730 8.1190171 900_at 2.2195445 2.8295452 3.4196709 1.8527308 901_g_at 5.7545168 5.0468389 5.6245357 5.8502142 902_at 6.6209798 4.3006058 3.7374849 4.5122710 903_at 8.7702203 8.7086162 9.1770804 9.2294808 904_s_at 7.0591976 5.1820527 8.5599538 9.0039754 905_at 11.9491289 11.9910444 11.6898046 11.7410571 906_at 6.3845652 6.9248605 6.8864277 6.8929933 907_at 7.6886424 7.1824391 7.2111292 7.8443307 908_at 8.2939290 7.7437175 6.5572648 6.8561620 909_g_at 7.4574221 7.6717804 5.3368385 3.2790867 910_at 8.0251156 7.3886445 12.1181993 12.6590912 911_s_at 12.8411078 12.5812833 13.4047543 13.1897043 912_s_at 5.6141964 4.9262996 6.0763124 6.0921603 913_at 6.7208538 6.0122446 2.0393705 6.0687166 914_g_at 2.8717200 2.8780858 2.1747980 3.6086332 915_at 11.1758828 10.8752733 10.1276721 9.6699940 916_at 8.4391105 9.8415047 9.1278395 10.2686699 917_g_at 8.7850470 8.0194363 8.4079739 8.7469938 918_at 10.2785296 9.8138168 8.8535422 9.3859466 919_at 8.3942796 8.3167995 7.1161269 8.3410835 920_at 8.0889058 7.9325313 5.7769296 6.8136452 921_s_at 6.6822631 7.0344140 5.4208743 6.3295713 922_at 13.2061191 13.0390407 13.0401613 12.9557347 923_at 7.5510308 8.1929780 5.4391951 7.6878229 924_s_at 9.7703859 9.7318225 9.2803441 9.6172897 925_at 12.9560996 12.3519429 12.5787333 12.0782950 926_at 7.4637770 6.7971648 5.2243658 6.6081742 927_s_at 10.3244430 10.5212960 9.2061603 9.5604950 928_at 3.8363711 3.2643991 3.8174267 4.1214598 929_at 7.1217021 7.4638187 5.7185762 6.9176704 930_at 7.4004462 6.6917953 4.2889635 6.4286234 931_at 5.3398771 6.2052656 1.7351899 2.1978462 932_i_at 10.4989823 10.4795489 9.8537563 10.1177851 933_f_at 9.1726182 8.9245080 8.3652713 8.9647960 934_at 7.1747955 7.3526983 7.0410866 8.1855756 935_at 11.5199937 11.2128601 11.0694535 10.7521910 936_s_at 5.9295903 5.0379136 4.3691382 4.6480071 937_at 5.3701385 6.4737718 5.1513922 6.7835825 [ reached getOption("max.print") -- omitted 126 rows ] 
par(mfrow=c(1,2))
log2d<-density(log2e_mas5)
plot(log2d)
boxplot(log2e_mas5)
Image in a Jupyter notebook
setwd("~/Autumn2016/Week5/data_wk_5")

load("eset_puma.RDA")
ls()
[1] "affybatch.estrogen" "d1" "d2" [4] "e_mas5" "e_rma" "eset_estrogen_puma" [7] "eset_mas5" "eset_rma" "log2d" [10] "log2e_mas5" 
show(eset_estrogen_puma)
Loading required package: puma Loading required package: oligo Loading required package: oligoClasses Welcome to oligoClasses version 1.32.0 Attaching package: ‘oligoClasses’ The following object is masked from ‘package:affy’: list.celfiles Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 Loading required package: IRanges Loading required package: XVector ================================================================================ Welcome to oligo version 1.34.2 ================================================================================ Attaching package: ‘oligo’ The following objects are masked from ‘package:affy’: intensity, MAplot, mm, mm<-, mmindex, pm, pm<-, pmindex, probeNames, rma Loading required package: mclust Package 'mclust' version 5.2 Type 'citation("mclust")' for citing this R package in publications.
exprReslt (storageMode: lockedEnvironment) assayData: 12625 features, 8 samples element names: exprs, se.exprs protocolData: none phenoData sampleNames: low10-1.cel low10-2.cel ... high48-2.cel (8 total) varLabels: estrogen time.h varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: hgu95av2 
e_mmgmos<-exprs(eset_estrogen_puma)
show(e_mmgmos)
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0.431699090 695_at -7.450489e-01 -0.346880053 696_at -3.020900e+00 -4.054947390 697_f_at -1.779906e+00 -2.973084218 698_f_at 3.398569e-02 1.574933373 699_s_at 4.676471e-01 2.594872056 700_s_at 4.026293e+00 3.570400011 701_s_at 1.369276e-01 2.905675610 702_f_at 3.297626e+00 3.890674732 703_at -1.509700e+00 -0.736632358 704_at -1.013959e+00 1.600538930 705_at -1.320210e-01 -0.380908046 706_at 1.634679e+00 1.034539154 707_s_at -2.191962e+00 -4.372886390 708_at -3.532509e+00 -3.723098372 709_at 5.950437e+00 5.834121214 710_at -2.392606e+00 -1.566953799 711_at -4.187640e+00 -4.413889712 712_s_at 2.359271e+00 2.367084124 713_at 1.062268e+00 2.526810523 714_at 2.438264e+00 3.231379652 715_s_at 2.603851e+00 3.543606701 716_at 2.320490e+00 3.223071600 717_at 2.248360e+00 1.501223059 718_at 2.751066e+00 2.067111081 719_g_at 3.047286e+00 2.975977279 720_at 3.472225e+00 3.469647168 721_g_at 4.386034e+00 5.004641192 722_at 2.537896e+00 2.607038072 723_s_at 6.839349e+00 6.614688180 724_at 6.138588e-01 1.384021022 725_i_at 3.351314e+00 4.298303447 726_f_at 2.578674e+00 3.173626477 727_at 2.182445e+00 3.084554934 728_at -8.175088e-01 1.170366555 729_i_at 4.493470e+00 4.434202449 730_r_at 1.259492e+00 1.101716152 731_f_at -1.362587e+00 1.377433229 732_f_at 8.134562e-01 2.202270843 733_at -1.974586e-01 0.266968527 734_at -1.661212e-01 -1.639168930 735_s_at 2.834731e+00 3.171826699 736_f_at 2.562852e+00 2.493164088 737_at -3.192856e+00 -3.365548909 738_at 3.732141e+00 2.923249465 739_at 1.419378e+00 0.682197579 740_at 8.624761e-01 0.688178282 741_g_at -1.921623e+00 -1.418632070 742_at -2.707397e+00 -3.021034314 743_at -3.568361e+00 -1.466634224 744_at 2.142336e+00 2.484385454 745_at 5.093164e+00 4.410004020 746_at -2.643677e+00 1.027703229 747_at -1.460264e+00 -0.713851096 748_s_at 1.999489e+00 1.046575451 749_at 5.267783e+00 5.096830944 750_at 4.187885e-03 -0.005130334 751_at 4.809796e+00 4.735911065 752_s_at 6.050541e+00 5.832008308 753_at -9.300328e-01 -1.709427612 754_s_at 3.594729e+00 3.281028153 755_at 2.376403e+00 1.962993872 756_at -2.018446e+00 -0.723178803 757_at 3.468221e+00 3.582790340 758_at 5.596432e-01 -0.865326758 759_at -2.576487e+00 0.212365086 760_at 3.285787e+00 2.807582272 761_g_at 7.648497e-01 -0.939225827 762_f_at 4.291815e+00 3.895181028 763_at 4.424696e+00 4.064943360 764_s_at -9.476009e-01 -1.767845147 765_s_at 9.494903e-01 -0.246127186 766_at 3.854514e+00 3.853711708 767_at -2.375878e+00 0.441674508 768_at 1.484513e+00 -1.704842879 769_s_at 8.603104e+00 8.130323198 770_at 3.403856e+00 3.729651642 771_s_at 1.181179e+00 0.003355644 772_at 3.375894e+00 3.709843462 773_at -4.330620e+00 -2.524284283 774_g_at -5.379124e+00 -4.432468756 775_at -2.153195e+00 -1.689791913 776_at 4.673707e+00 4.457157998 777_at 5.279652e+00 5.835854213 778_s_at 3.635120e+00 3.571397109 779_at -3.160740e+00 -3.966068369 780_at 2.745347e-01 -1.838843401 781_at 4.146109e+00 3.018871936 782_at 3.824771e+00 3.273152772 783_at 4.099707e+00 4.175254436 784_g_at 4.168531e+00 4.012918015 785_at 2.647863e+00 2.196489874 786_at 3.766394e+00 3.702771608 789_at 2.011576e+00 1.534064825 790_at -1.987849e+00 -1.969620591 791_g_at -2.260407e+00 -0.261262649 792_s_at 2.750866e+00 4.178698720 793_at 2.205598e+00 2.890726962 794_at 3.357612e+00 2.616472337 795_s_at 1.299823e+00 -0.428837954 796_i_at -4.603033e-02 -2.868364899 797_at -3.566131e+00 -4.558342046 798_at 4.251125e+00 4.052121107 799_at 3.101017e+00 3.156366703 800_g_at 6.652403e-02 2.106168422 801_at -1.509779e+00 -0.308641164 802_at 3.098321e+00 2.384884688 803_at -2.428078e+00 -4.284326282 804_s_at 1.757630e+00 2.168550207 805_at -3.812994e+00 -3.614375339 806_at 2.568200e+00 2.072028395 807_at -1.246596e+00 -1.353025518 808_at -3.387330e+00 -2.751192074 809_at 3.511125e+00 3.733273227 810_at 3.916052e+00 4.039678699 811_at 5.920002e+00 5.160384410 812_at 3.398594e+00 3.277824585 813_at -4.434143e+00 -2.401489071 814_s_at -2.808402e+00 -0.621262802 815_at 6.510912e-01 -0.697571695 816_g_at 4.550378e+00 4.326768556 817_at 1.508614e+00 2.270362582 818_s_at 3.728107e+00 2.780897160 819_at -3.027873e+00 -3.788380789 820_at 4.538175e+00 3.961990226 821_s_at -1.853986e+00 -0.025581709 822_s_at 2.094769e+00 2.155361814 823_at -1.695860e+00 0.242073667 824_at 5.745296e+00 5.220094528 825_at -1.004053e-01 2.128108098 826_at 2.369958e+00 3.714954520 827_s_at -6.744956e-04 -1.704142625 828_at 3.255467e-01 -1.767871952 829_s_at -5.595378e+00 -2.574178487 830_at 5.794212e-01 1.589081108 831_at 1.990723e+00 1.917175963 832_at 5.313270e+00 5.573836072 833_at 2.371078e+00 2.884382440 834_at -1.242487e+00 0.050453814 835_at 4.897453e+00 4.980504611 836_at 8.762624e-01 1.522898321 837_s_at 3.849169e+00 3.432644809 838_s_at 7.242847e+00 7.049605728 839_at -3.852555e+00 -3.777702058 840_at 3.725814e+00 3.207284653 841_at -3.039180e+00 -2.255754371 842_at 4.128251e+00 3.698223403 843_at 4.619195e+00 4.190681644 844_at 2.223522e+00 2.486992360 845_at 1.749038e+00 2.222570184 846_s_at 2.767199e+00 2.911254096 847_at 3.746793e+00 3.399859479 848_at 8.744728e-02 1.899908839 849_g_at -8.095956e-01 -1.576528975 850_r_at 1.113899e+00 2.910847736 851_s_at 4.494537e+00 3.944536391 852_at -3.718456e-01 1.148343156 853_at 3.963076e+00 2.713654605 854_at -2.867646e-01 1.410516163 855_at 3.651614e+00 3.731444237 856_at -1.516739e-01 1.262084036 857_at 3.792568e+00 3.569432201 858_at 4.783996e+00 4.493543691 859_at 3.675653e+00 3.445474596 860_at 4.499043e+00 3.443680821 861_g_at 3.596453e+00 3.443545415 862_at -7.825372e-01 -1.016009107 863_g_at 1.524196e+00 1.795713136 864_at 3.954624e+00 3.519949283 865_at 2.225308e+00 2.645866133 866_at 2.029410e+00 1.519309015 867_s_at -2.137786e+00 2.763692019 868_at 5.364510e+00 4.765762311 869_at 4.893856e+00 4.383430492 870_f_at 6.419955e+00 6.328240094 871_s_at 1.025864e+00 1.772348641 872_i_at 3.467197e+00 3.072376218 873_at 6.832250e-01 -2.721327106 874_at 1.874717e+00 1.584848104 875_g_at 6.997206e-01 0.601778130 876_at 6.228760e-01 0.761886760 877_at 1.932179e+00 1.118909973 878_s_at 2.900610e+00 3.143080711 879_at 7.932116e-01 1.388173283 880_at 6.456508e+00 6.367940525 881_at -1.639189e+00 -1.340424446 882_at 5.914318e+00 6.101252077 883_s_at 4.389391e+00 4.112266064 884_at 4.727439e+00 5.149537677 885_g_at 3.880060e+00 3.540726804 886_at 1.718039e-01 1.149985626 887_at 4.500361e+00 4.490187308 888_s_at 3.332240e+00 2.760311222 889_at -5.099716e-01 1.265142913 890_at 4.759457e+00 4.299349797 891_at 4.679866e+00 4.208973798 892_at 5.271242e-01 0.308346820 893_at 7.547776e+00 7.459339750 894_g_at 7.563881e+00 7.365529415 895_at 9.516244e+00 9.337595265 896_at -4.121661e-01 -2.118147667 897_at 3.716075e+00 2.694780800 898_s_at 2.979434e+00 4.071859782 899_at 2.077481e+00 1.937481913 900_at -1.464988e+00 -3.272236449 901_g_at -1.059543e+00 -0.654021972 902_at 1.185154e-01 -1.526963542 903_at 3.978904e+00 3.512754375 904_s_at 4.322441e+00 4.390377693 905_at 6.551259e+00 6.449117919 906_at 1.974926e+00 2.170334400 907_at 1.246359e+00 1.178122539 908_at 2.361872e+00 2.559109816 909_g_at 1.162991e+00 0.311122725 910_at 6.812401e+00 6.918208093 911_s_at 8.111327e+00 7.752644325 912_s_at 1.779838e+00 1.204240604 913_at -1.965343e+00 1.665460919 914_g_at -1.715643e+00 -2.791689091 915_at 5.136998e+00 4.825736791 916_at 1.993921e+00 3.160431706 917_g_at 1.080283e+00 1.159702748 918_at 3.595768e+00 4.002955059 919_at 2.357924e+00 3.560042566 920_at 1.946023e+00 1.883500811 921_s_at -2.219777e+00 -2.147782322 922_at 7.581929e+00 7.386928886 923_at -1.366949e+00 2.187834314 924_s_at 4.455768e+00 4.283354929 925_at 6.905357e+00 6.655240049 926_at -8.164230e-01 0.492528224 927_s_at 3.878547e+00 3.844181881 928_at -2.249253e+00 -1.399594403 929_at -1.794567e+00 0.709362836 930_at -2.054262e+00 -0.992004050 931_at -1.583752e+00 -2.426800797 932_i_at 5.017734e+00 5.208808783 933_f_at 4.100688e+00 4.054926405 934_at 1.396233e+00 2.602929907 935_at 5.976570e+00 5.700719914 936_s_at 1.143364e+00 0.293785959 937_at 6.505608e-01 1.809141560 [ reached getOption("max.print") -- omitted 126 rows ] 
log2e_mmgmos<-log2(e_mmgmos)
show(log2e_mmgmos)
Warning message in eval(expr, envir, enclos): “NaNs produced”
low10-1.cel low10-2.cel high10-1.cel 100_g_at 2.190200e+00 2.337501273 2.109271e+00 1000_at 2.816426e+00 2.754252303 2.623717e+00 1001_at NaN NaN NaN 1002_f_at NaN NaN NaN 1003_s_at NaN NaN NaN 1004_at -3.678142e+00 -2.481912223 NaN 1005_at 2.428289e+00 2.382686252 1.606819e+00 1006_at -3.501635e-01 -0.928262554 -1.463531e-01 1007_s_at 3.164419e+00 3.140766794 3.057897e+00 1008_f_at 2.468918e+00 2.875980726 2.842432e+00 1009_at 2.842557e+00 2.860230209 2.999319e+00 101_at NaN NaN NaN 1010_at NaN NaN NaN 1011_s_at 2.422999e+00 2.296840444 2.487340e+00 1012_at 1.272598e+00 -0.375665013 -2.924880e+00 1013_at 1.651158e+00 1.595197460 1.620571e+00 1014_at 2.357720e+00 2.393695812 2.468164e+00 1015_s_at NaN NaN NaN 1016_s_at NaN NaN -1.306802e+00 1017_at -2.110777e-01 -2.113701817 -6.738310e-01 1018_at NaN NaN NaN 1019_g_at 8.129754e-01 1.069624105 8.424082e-01 102_at 2.787830e-01 -0.318900375 -7.082417e-01 1020_s_at 3.021334e+00 3.003261945 2.912948e+00 1021_at 2.722783e-01 0.504289295 NaN 1022_f_at NaN NaN NaN 1023_at NaN NaN NaN 1024_at NaN -0.392716686 NaN 1025_g_at 2.442102e+00 2.442453058 1.914002e+00 1026_s_at NaN NaN NaN 1027_at NaN NaN NaN 1028_at NaN -3.375680828 7.485453e-01 1029_s_at NaN NaN NaN 103_at NaN -1.843197437 NaN 1030_s_at 2.941719e+00 2.902135561 2.907839e+00 1031_at 2.009680e+00 2.051365771 2.106400e+00 1032_at 1.249810e+00 0.996268322 5.203905e-02 1033_g_at NaN NaN NaN 1034_at 2.633527e+00 2.660435716 2.300107e+00 1035_g_at 2.546228e+00 2.498132512 1.968328e+00 1036_at NaN NaN NaN 1037_at 6.427969e-01 0.595138919 -3.064840e+00 1038_s_at 2.066956e+00 1.977743765 1.825500e+00 1039_s_at 2.338084e+00 2.174790496 2.327155e+00 104_at NaN 1.397183600 1.451480e+00 1040_s_at 2.752830e-01 0.168690378 6.738886e-01 1041_at -1.109832e-01 -2.945489729 NaN 1042_at -1.385474e+00 -0.312939579 NaN 1043_s_at NaN NaN NaN 1044_s_at 2.376195e+00 2.345135960 2.164633e+00 1045_s_at 2.036720e+00 2.027043768 2.057824e+00 1046_at 2.262166e+00 2.224817557 2.058141e+00 1047_s_at -9.480247e-02 0.701937551 5.483664e-01 1048_at 4.003301e-02 0.859239037 -1.098487e+00 1049_g_at NaN NaN NaN 105_at NaN NaN NaN 1050_at NaN NaN NaN 1051_g_at -2.131644e+00 -2.430523927 NaN 1052_s_at 2.647063e+00 2.661757664 2.467371e+00 1053_at 1.431702e+00 1.623370965 2.515610e+00 1054_at -4.604452e+00 -3.474211770 1.646665e+00 1055_g_at NaN -0.412327249 2.389883e+00 1056_s_at NaN NaN NaN 1057_at 3.101234e+00 3.086235642 2.944127e+00 1058_at 1.154809e+00 -3.879357426 1.163279e+00 1059_at NaN NaN NaN 106_at NaN NaN NaN 1060_g_at NaN NaN NaN 1061_at NaN NaN NaN 1062_g_at NaN NaN NaN 1063_s_at 2.649156e-01 NaN NaN 1064_at 2.305061e+00 2.226028454 2.289280e+00 1065_at NaN -0.613241525 3.792433e-01 1066_at -4.244011e-01 -0.597799113 NaN 1067_at 7.307475e-01 0.540754104 -2.354371e+00 1068_g_at NaN NaN NaN 1069_at -1.542758e-01 NaN NaN 107_at -7.717267e+00 NaN NaN 1070_at 1.609503e+00 1.412177238 1.384699e+00 1071_at -2.402672e-01 1.025686993 -1.109263e+00 1072_g_at 2.270129e+00 2.189323702 1.957237e+00 1073_at 2.595626e+00 2.536968067 2.614974e+00 1074_at 2.619269e+00 2.537553383 2.577157e+00 1075_f_at 1.107858e-02 -1.292070647 NaN 1076_at 1.906184e+00 1.885838639 1.349028e+00 1077_at NaN NaN NaN 1078_at 2.026196e+00 1.959416663 1.866208e+00 1079_g_at 2.145750e+00 2.251569069 2.067489e+00 108_g_at NaN -1.455353033 -1.547030e+00 1080_s_at NaN NaN NaN 1081_at 2.961429e+00 2.952766080 2.927051e+00 1082_at 1.013444e+00 1.007200487 1.647270e+00 1083_s_at -1.859864e+00 0.248237038 -1.242260e+00 1084_at NaN NaN NaN 1085_s_at 2.188070e+00 2.236128203 2.162148e+00 1086_at NaN NaN NaN 1087_at 1.775482e+00 1.866627072 NaN 1088_at NaN NaN NaN 1089_i_at -1.829316e-01 0.557482405 7.926430e-02 109_at 2.247400e+00 2.211674673 2.385139e+00 1090_f_at NaN -0.655013538 -3.627411e-01 1091_at 2.588884e+00 2.536147407 2.513760e+00 1092_at -2.307801e+00 0.991054979 -7.106288e-01 1093_at NaN -0.477182765 5.275032e-01 1094_g_at NaN -0.452538361 5.226952e-01 1095_s_at NaN NaN NaN 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-6.018460e-01 1919_at NaN NaN NaN 192_at 2.788523e+00 2.752351181 2.745013e+00 1920_s_at 2.345255e+00 2.402840806 2.257468e+00 1921_at -3.303066e+00 NaN NaN 1922_g_at -2.309767e+00 0.543702665 -2.083939e+00 1923_at 1.241893e+00 1.187257397 1.552592e+00 1924_at 2.279576e+00 2.260278952 2.280118e+00 1925_at 2.292477e+00 2.158148257 2.156911e+00 1926_at 1.621268e+00 1.603901920 3.809391e-01 1927_s_at NaN NaN NaN 1928_s_at 1.960816e+00 1.884442231 1.693962e+00 1929_at -2.142576e+00 0.639811895 NaN 193_at 2.132373e+00 2.241467767 2.385322e+00 1930_at 1.504668e+00 1.476744123 -5.156247e-01 1931_at NaN NaN NaN 1932_at 1.728633e+00 1.785815231 -4.575958e-01 1933_g_at 2.704528e+00 2.684878444 2.461214e+00 1934_s_at NaN NaN NaN 1935_at 1.608365e+00 1.237263328 1.586149e+00 1936_s_at 2.046313e+00 1.962556743 2.530206e+00 1937_at 2.131754e+00 2.206832298 2.062848e+00 1938_at -2.167394e+00 -0.943114290 NaN 1939_at 2.128003e+00 2.086995602 2.146260e+00 194_at -6.779017e-02 -2.629750423 NaN 1940_at 2.191588e+00 2.085646183 2.130302e+00 1941_at NaN NaN NaN 1942_s_at 2.787288e+00 2.777889304 2.978634e+00 1943_at 2.116247e+00 1.960152188 2.472913e+00 1944_f_at 1.420146e+00 1.880799100 2.244319e+00 1945_at 2.451478e+00 2.315613159 2.610308e+00 1946_at NaN NaN NaN 1947_g_at NaN NaN NaN 1948_f_at 7.808922e-01 0.307683170 1.032896e+00 1949_at NaN NaN NaN 195_s_at NaN NaN NaN 1950_s_at 2.217834e+00 2.366649027 2.051820e+00 1951_at NaN NaN NaN 1952_s_at 2.131432e+00 2.030636387 2.080831e+00 1953_at 2.658716e+00 2.593929243 2.528606e+00 1954_at -4.295369e-03 0.020612988 1.017746e+00 1955_s_at 1.917744e+00 1.811174117 1.049938e+00 1956_s_at NaN NaN NaN 1957_s_at -1.613222e-01 -0.152779571 NaN 1958_at NaN NaN NaN 1959_at 2.602491e+00 2.493039619 2.618958e+00 196_s_at NaN NaN NaN 1960_at NaN NaN NaN 1961_f_at NaN NaN NaN 1962_at NaN NaN NaN 1963_at -6.310659e+00 -0.911448864 NaN 1964_g_at NaN -0.970174926 NaN 1965_s_at NaN NaN NaN 1966_i_at NaN NaN NaN 1967_f_at 7.419726e-01 1.159677543 3.596748e-01 1968_g_at NaN NaN NaN 1969_s_at 2.369711e+00 2.285263249 2.091261e+00 197_at 2.768838e+00 2.759581814 2.748708e+00 1970_s_at 2.164456e+00 2.054946193 1.220508e+00 1971_g_at 1.512745e+00 0.616815635 1.083538e+00 1972_s_at NaN NaN NaN 1973_s_at 2.384981e+00 2.350591363 2.768075e+00 1974_s_at 2.267226e+00 2.248533270 2.189798e+00 1975_s_at NaN NaN -3.026299e+00 1976_s_at -1.176087e-01 0.734391486 -2.416610e+00 1977_s_at NaN NaN NaN 1978_at NaN NaN NaN 1979_s_at 2.289601e+00 2.198075885 2.489641e+00 198_g_at 3.076588e+00 3.079056999 3.040192e+00 1980_s_at 3.423190e+00 3.420219839 3.460821e+00 1981_s_at 1.851378e+00 1.731548081 2.110981e+00 1983_at NaN -1.822362530 -7.469438e-01 1984_s_at NaN NaN NaN 1985_s_at 3.080475e+00 3.066408725 3.289871e+00 1986_at 2.149024e+00 2.051445322 1.846278e+00 1987_at -1.016235e+00 0.728170610 NaN 1988_at NaN -1.446235840 NaN 1989_at -2.285088e+00 NaN 7.441622e-01 199_s_at 2.235711e+00 2.256149094 2.219976e+00 1990_g_at -2.224900e-02 NaN 1.499483e+00 1991_s_at 1.463660e+00 1.128572800 1.626793e+00 1992_at 1.329956e-01 -0.273773798 1.426266e-01 1993_s_at NaN NaN 2.982348e-01 1994_at 1.638613e+00 1.833984259 1.429490e+00 1995_at NaN NaN NaN 1996_s_at 1.158056e+00 1.101028401 3.299999e-01 1997_s_at 2.514027e+00 2.777343889 2.508623e+00 1998_i_at 1.833531e+00 1.969757876 2.135164e+00 1999_s_at 6.606954e-01 1.377414533 1.220254e+00 200_at NaN NaN NaN 2000_at 1.453340e+00 1.969116897 1.699920e+00 2001_g_at NaN -6.662756461 -2.010866e-01 2002_s_at NaN NaN NaN 2003_s_at 1.758955e+00 1.726172430 2.500955e+00 2004_at 2.510035e+00 2.387359541 2.309060e+00 2005_s_at 1.467964e+00 1.159704752 9.968127e-01 2006_at NaN NaN NaN 2007_g_at NaN NaN NaN 2008_s_at NaN -0.418254467 -3.762223e-01 2009_at 5.406304e-02 -0.451407175 NaN 201_s_at 3.156676e+00 3.166036556 3.141365e+00 2010_at 2.883319e+00 2.880075425 2.878225e+00 2011_s_at 1.821369e+00 1.893661173 NaN 2012_s_at 2.220322e+00 2.098532249 2.459541e+00 2013_at -6.114098e-02 1.197415323 1.460888e-01 2014_s_at NaN NaN NaN 2015_s_at 1.492640e+00 1.556840349 1.743648e+00 2016_s_at 3.507202e+00 3.523977756 3.516686e+00 2017_s_at 2.676959e+00 2.612034791 3.000649e+00 2018_at NaN NaN NaN 2019_s_at NaN NaN NaN 202_at 1.658305e+00 1.728364355 1.912429e+00 2020_at 2.882553e+00 2.882743334 3.210278e+00 2021_s_at 1.469223e+00 1.416664859 1.509778e+00 2022_at NaN NaN NaN 2023_g_at NaN -2.506635918 NaN 2024_s_at NaN NaN NaN 2025_s_at 3.002481e+00 2.995567800 3.052181e+00 2026_at NaN NaN NaN 2027_at NaN -0.930811630 NaN 2028_s_at 1.839365e+00 1.542380656 2.431769e+00 2029_at 6.179405e-01 0.153308679 1.419802e+00 203_at 1.413767e+00 1.196286440 -8.542991e-01 2030_at NaN NaN NaN 2031_s_at 2.981533e+00 2.997631691 2.397973e+00 2032_s_at NaN NaN NaN 2033_s_at 1.386938e+00 1.158146475 1.256556e+00 2034_s_at NaN NaN NaN 2035_s_at 3.469970e+00 3.458503892 3.386427e+00 2036_s_at 1.356647e+00 0.390337975 2.365781e+00 2037_s_at 2.991579e+00 2.977601187 2.971747e+00 2038_g_at NaN 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35559_at NaN NaN 35560_at NaN NaN 35561_at NaN NaN 35562_at 1.427326e+00 -0.1182381396 35563_at NaN -1.2600638246 35564_at NaN NaN 35565_at NaN NaN 35566_f_at 9.247160e-01 0.4487324540 35567_at 9.857313e-02 NaN 35568_at -1.241410e-01 NaN 35569_at 8.310053e-01 1.2219328848 35570_at NaN 0.0160683551 35571_at 1.375491e+00 1.3870713064 35572_f_at 1.314697e+00 1.1415310160 35573_r_at 5.880088e-01 0.6497692529 35574_i_at NaN NaN 35575_f_at NaN 0.8267615375 35576_f_at 2.474645e+00 2.5406014634 35577_at NaN NaN 35578_at NaN NaN 35579_at 1.115721e+00 0.2483929839 35580_at NaN NaN 35581_at 1.049403e-01 NaN 35582_at NaN NaN 35583_at NaN NaN 35584_s_at NaN NaN 35585_at NaN NaN 35586_at NaN NaN 35587_at NaN -0.0623627684 35588_at 1.780620e+00 1.7563332098 35589_at NaN NaN 35590_s_at 1.525914e+00 1.8496025512 35591_at 3.843482e-01 0.3550175982 35592_at 7.020229e-01 NaN 35593_at NaN NaN 35594_at -2.066939e-01 -0.0044016511 35595_at 1.385867e+00 1.4395806774 35596_at NaN -2.4680453045 35597_at NaN 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NaN 37493_at -2.856929e+00 NaN 37494_at NaN NaN 37495_at NaN NaN 37496_at NaN NaN 37497_at 8.814897e-01 NaN 37498_at NaN NaN 37499_at 3.834163e-01 NaN 375_at 1.771468e+00 1.5904899244 37500_at NaN NaN 37501_at 1.621855e+00 1.2605970745 37502_at 5.309848e-01 -1.8461803539 37503_at 1.642349e+00 1.4857614070 37504_at 1.340146e+00 1.4551216352 37505_at -2.924961e-01 0.6101333868 37506_at 2.094138e+00 1.9469541972 37507_i_at 2.145950e+00 2.0028344403 37508_f_at 2.378689e+00 2.3154036848 37509_at 1.540319e+00 1.3531937434 37510_at 1.700834e+00 1.0365186272 37511_at 1.803430e+00 1.6805230970 37512_at NaN NaN 37513_at 1.095628e+00 2.1007065359 37514_s_at NaN NaN 37515_at NaN -1.4299399217 37516_at NaN NaN 37517_at 2.165964e+00 2.2888790839 37518_at 1.065164e+00 1.2191519573 37519_at 1.392157e+00 1.6962633180 37520_at 1.594515e+00 0.9821029849 37521_s_at 1.362382e+00 1.5879299140 37522_r_at NaN NaN 37523_at NaN NaN 37524_at NaN NaN 37525_at NaN NaN 37526_at NaN NaN 37527_at -4.541585e-01 1.1339156817 37528_at NaN NaN 37529_at 1.727714e+00 1.7053421351 37530_s_at -2.100014e+00 -2.1683291853 37531_at 1.498933e+00 2.0589691050 37532_at 1.823300e+00 1.4785632305 37533_r_at NaN NaN 37534_at -2.561259e+00 NaN 37535_at 1.653119e+00 1.3417583581 37536_at -3.177778e-01 NaN 37537_at 1.338919e+00 1.1599852931 37538_at NaN NaN 37539_at NaN NaN 37540_at NaN NaN 37541_at -8.259908e+00 1.7768316178 37542_at 1.641040e+00 1.2732731385 37543_at 1.424943e+00 1.3313491613 37544_at 1.320360e+00 1.2548769474 37545_at 2.244539e+00 2.2175835711 37546_r_at NaN 1.3502028867 37547_at NaN NaN 37548_at NaN NaN 37549_g_at 6.460734e-01 0.9283637936 37550_at 1.021262e+00 0.2040150290 37551_at 2.439873e+00 2.4229485959 37552_at 1.711615e+00 1.5192919962 37553_at 1.756397e+00 1.6522464364 37554_at 3.354922e-01 -1.4309595540 37555_at 2.065926e+00 1.8809572679 37556_at NaN NaN 37557_at 2.555798e+00 2.4334741622 37558_at -5.987916e-01 NaN 37559_at NaN NaN 37560_at NaN NaN 37561_at 1.894879e+00 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NaN 37595_at NaN NaN 37596_at -2.018167e+00 -0.0996402795 37597_s_at 2.354398e+00 2.2137498477 37598_at NaN NaN 37599_at NaN NaN 376_at 2.347327e+00 2.3335016075 37600_at 7.148826e-01 -1.0169373526 37601_at NaN NaN 37602_at NaN NaN 37603_at NaN NaN 37604_at 4.350886e-01 NaN 37605_at NaN NaN 37606_at 5.869423e-01 -1.6573082424 37607_at NaN NaN 37608_g_at 8.334140e-01 -4.7768732259 37609_at 1.939743e+00 1.6764480486 37610_at 2.499706e+00 2.4506754693 37611_at NaN NaN 37612_at NaN NaN 37613_at NaN NaN 37614_g_at NaN NaN 37615_at 1.452686e+00 1.5718720584 37616_at 1.628909e+00 1.2964324480 37617_at 1.116175e+00 0.5994294175 37618_at 1.949875e+00 1.9064627508 37619_at 2.320112e+00 2.0869401892 37620_at 1.723834e+00 1.5926982400 37621_at NaN NaN 37622_r_at NaN NaN 37623_at NaN NaN 37624_at NaN -1.4506409265 37625_at NaN NaN 37626_at NaN NaN 37627_g_at NaN NaN 37628_at 2.139008e+00 1.9823257673 37629_at 1.139794e-01 1.5720146160 37630_at NaN NaN 37631_at 7.406440e-01 1.4519703239 37632_s_at 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38388_at 2.043891e+00 1.9909898751 38389_at 4.601727e-01 0.0702333774 38390_at 1.829859e+00 1.6685717586 38391_at 1.874026e+00 1.5741853042 38392_at 2.406316e+00 2.3068734178 38393_at 1.809718e+00 1.6232424924 38394_at 2.219638e+00 1.9871977922 38395_at 2.161237e+00 1.9632618086 38396_at NaN NaN 38397_at 2.545479e+00 2.4604743958 38398_at 2.278830e+00 2.2650574625 38399_at 2.466912e+00 2.2774197984 384_at 2.296847e+00 2.0729042190 38400_at 2.275179e+00 2.1368851788 38401_s_at 1.971844e+00 1.7804229634 38402_at 1.690723e+00 1.4607868949 38403_at 2.018888e+00 1.8799796220 38404_at NaN NaN 38405_at NaN -2.0292181276 38406_f_at -2.073699e-01 1.6556496071 38407_r_at NaN NaN 38408_at NaN NaN 38409_at -1.193348e+00 -0.0854551655 38410_at 2.442221e+00 2.3124236967 38411_at 7.872586e-01 NaN 38412_at 2.422700e+00 2.3922410608 38413_at 2.604253e+00 2.5300801884 38414_at 2.709803e+00 2.6693991007 38415_at 1.640513e+00 1.3568422755 38416_at 2.220899e+00 2.0186149932 38417_at 2.162258e+00 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NaN 38547_at NaN NaN 38548_at NaN NaN 38549_at NaN NaN 38550_at 6.035537e-01 NaN 38551_at 2.326105e+00 2.1912463888 38552_f_at 1.563752e+00 1.5479543205 38553_r_at 1.058199e+00 1.4530828149 38554_at 3.829588e-01 -0.4585980518 38555_at NaN NaN 38556_at 5.740914e-01 NaN 38557_at -1.404690e+00 -0.3568650318 38558_at 2.083275e+00 2.3219148868 38559_at 1.167707e+00 1.2479787956 38560_at -5.207202e-01 0.8713091559 38561_at NaN NaN 38562_g_at -2.373975e-01 NaN 38563_at 1.982811e+00 1.8675744878 38564_at 2.075919e+00 2.0423883100 38565_at NaN -0.8922796838 38566_at 1.636957e+00 1.6077965590 38567_at NaN NaN 38568_at 1.737376e+00 1.1635534374 38569_at -1.797064e+00 NaN 38570_at 1.745901e-01 1.1763357661 38571_at 1.959576e+00 1.3763681914 38572_at NaN NaN 38573_at 9.099091e-01 0.8692328398 38574_at -2.481578e-01 1.3068701370 38575_at NaN NaN 38576_at 2.394446e+00 2.2206583038 38577_at NaN NaN 38578_at NaN NaN 38579_at NaN NaN 38580_at NaN 1.0769878971 38581_at 1.239708e+00 0.8165060978 38582_at 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-0.5007142884 38678_at 1.654376e+00 0.9557088185 38679_g_at 2.969310e+00 2.8874100238 38680_at 1.792988e+00 1.6151312843 38681_at 2.822703e+00 2.7445321317 38682_at 1.101366e+00 NaN 38683_s_at 1.814170e+00 1.5501326430 38684_at 9.657034e-01 -0.9398427990 38685_at 1.149107e+00 -0.9668896020 38686_at 2.505317e+00 2.4474006223 38687_at 2.185041e+00 1.9707553884 38688_at 2.483732e+00 2.3618011371 38689_at 2.330256e+00 2.1021689238 38690_at 2.084565e+00 2.0845995708 38691_s_at -6.731519e-01 -1.1034547199 38692_at 1.728812e+00 1.5939518514 38693_at 1.297904e+00 1.0696492886 38694_at 9.286733e-01 NaN 38695_at 2.349503e+00 2.3041228786 38696_at NaN NaN 38697_at 2.193049e+00 1.7018075706 38698_at 1.673561e+00 1.4193572991 38699_at NaN NaN 387_at 1.765514e+00 1.3725549025 38700_at 2.537897e+00 2.5409998224 38701_at 1.168010e+00 1.6122511119 38702_at 2.658514e+00 2.5502474725 38703_at 2.633503e+00 2.5108223510 38704_at 1.846615e+00 1.6684690771 38705_at 2.212408e+00 1.9863215449 38706_at 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38862_at 2.724351e-01 0.3277388470 38863_at 2.146918e+00 2.2547297415 38864_at 2.105741e+00 1.6775828501 38865_at 6.696188e-01 1.3598506055 38866_at -3.705301e+00 -3.7689142677 38867_g_at NaN NaN 38868_at NaN NaN 38869_at NaN NaN 38870_at -3.072683e+00 -1.3646762131 38871_at NaN -0.6159276240 38872_at NaN NaN 38873_at NaN NaN 38874_s_at NaN NaN 38875_r_at 2.585514e+00 2.5047007949 38876_at 5.756300e-01 0.2113237167 38877_s_at NaN NaN 38878_at 3.274812e-02 NaN 38879_at NaN NaN 38880_at -8.404210e-01 0.5446767705 38881_i_at 2.013584e+00 1.9032107269 38882_r_at 2.390791e+00 2.3488848762 38883_at NaN NaN 38884_at NaN NaN 38885_at 3.024025e-01 1.0694393918 38886_i_at NaN NaN 38887_r_at NaN NaN 38888_at -1.616241e+00 -4.2769808485 38889_at NaN 0.9193061860 38890_at NaN NaN 38891_at NaN NaN 38892_at 1.138834e-01 0.8847226941 38893_at 3.565501e-01 NaN 38894_g_at -1.532202e+00 -0.7056289986 38895_i_at NaN NaN 38896_at 9.135731e-01 -0.3363060586 38897_at -4.647482e-01 -1.5710983388 38898_at 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877_at 9.502285e-01 0.1620939623 878_s_at 1.536357e+00 1.6521793195 879_at -3.342223e-01 0.4731876679 880_at 2.690754e+00 2.6708268615 881_at NaN NaN 882_at 2.564212e+00 2.6091053378 883_s_at 2.134021e+00 2.0399336100 884_at 2.241059e+00 2.3644429136 885_g_at 1.956079e+00 1.8240455323 886_at -2.541165e+00 0.2016158292 887_at 2.170041e+00 2.1667756283 888_s_at 1.736492e+00 1.4648309386 889_at NaN 0.3393003636 890_at 2.250797e+00 2.1041184934 891_at 2.226467e+00 2.0734685285 892_at -9.237851e-01 -1.6973741278 893_at 2.916052e+00 2.8990479385 894_g_at 2.919127e+00 2.8807892262 895_at 3.250392e+00 3.2230510568 896_at NaN NaN 897_at 1.893780e+00 1.4301679252 898_s_at 1.575038e+00 2.0256878817 899_at 1.054835e+00 0.9541828426 900_at NaN NaN 901_g_at NaN NaN 902_at -3.076853e+00 NaN 903_at 1.992371e+00 1.8126027016 904_s_at 2.111846e+00 2.1343450565 905_at 2.711772e+00 2.6891018487 906_at 9.817983e-01 1.1179173470 907_at 3.177193e-01 0.2364896046 908_at 1.239931e+00 1.3556420576 909_g_at 2.178401e-01 -1.6844443180 910_at 2.768163e+00 2.7903984092 911_s_at 3.019938e+00 2.9546884785 912_s_at 8.317460e-01 0.2681236679 913_at NaN 0.7359215004 914_g_at NaN NaN 915_at 2.360926e+00 2.2707492291 916_at 9.956085e-01 1.6601216399 917_g_at 1.114087e-01 0.2137550644 918_at 1.846300e+00 2.0010654189 919_at 1.237517e+00 1.8318944909 920_at 9.605284e-01 0.9134166545 921_s_at NaN NaN 922_at 2.922565e+00 2.8849746889 923_at NaN 1.1295034859 924_s_at 2.155674e+00 2.0987412273 925_at 2.787716e+00 2.7344907039 926_at NaN -1.0217216947 927_s_at 1.955516e+00 1.9426765962 928_at NaN NaN 929_at NaN -0.4954043466 930_at NaN NaN 931_at NaN NaN 932_i_at 2.327036e+00 2.3809534763 933_f_at 2.035866e+00 2.0196757305 934_at 4.815397e-01 1.3801364624 935_at 2.579318e+00 2.5111441211 936_s_at 1.932851e-01 -1.7671626475 937_at -6.202441e-01 0.8553052988 [ reached getOption("max.print") -- omitted 126 rows ] 
library(limma)

limma::plotMA(log2e_mas5)
Image in a Jupyter notebook