Kernel: R
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Exercise 1
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mas5() executes the command for MAS5.0 expression measure. This function converts an instance of AffyBatch into an instance of ExpressionSet using the implementation of Affymetrix's MAS5.0 expression measure. Using mas5(object, normalize = TRUE, sc = 500, analysis = "absolute", ...)
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rma() executes the command for Robust Multi-Array Average expression measure. This function conversts an AffyBatch object into an ExpressionSet object using the RMA expression measure. Using rma(object, subset=NULL, verbose=TRUE, destructive=TRUE, normalize=TRUE, background=TRUE, bgversion=2, ...)
Exercise 2
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[1] "/projects/ddda6a8e-2bca-47f5-b1d6-79b2c48d0e30/Autumn2016/Week4/data_wk4"
Exercise 3
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AffyBatch object
size of arrays=640x640 features (35221 kb)
cdf=HG_U95Av2 (12625 affyids)
number of samples=4
number of genes=12625
annotation=hgu95av2
notes=
The data shows the size of the array is 640x640 (35221kb), cdf maps each gene that is in the array (12625 genes), and there are 4 samples.
Exercise 4
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Background correcting
Normalizing
Calculating Expression
ExpressionSet (storageMode: lockedEnvironment)
assayData: 1 features, 4 samples
element names: exprs
protocolData: none
phenoData
sampleNames: 20A 20B 10A 10B
varLabels: liver sn19 scanner
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hgu95av2
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background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
12625 ids to be processed
| |
|####################|
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20A 20B 10A 10B
100_g_at 8.039969 7.891522 8.022329 7.910679
1000_at 7.790839 7.661209 7.716827 7.622688
1001_at 5.175568 5.067023 5.082672 5.091804
1002_f_at 5.916532 5.754500 5.816628 5.741990
1003_s_at 6.335194 6.010436 6.198295 6.133995
1004_at 6.390533 6.147808 6.357680 6.260663
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20A 20B 10A 10B
100_g_at 548.98527 433.2680 424.96155 393.97712
1000_at 809.08453 699.3555 808.41458 701.34489
1001_at 70.01311 109.4756 81.87722 90.15127
1002_f_at 161.94720 172.0894 138.57740 166.27219
1003_s_at 52.33766 101.3367 33.09268 31.61867
1004_at 211.22394 148.7227 161.71606 133.46727
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20A 20B 10A 10B
100_g_at 9.100624 8.759116 8.731189 8.621968
1000_at 9.660147 9.449882 9.658952 9.453980
1001_at 6.129553 6.774465 6.355390 6.494276
1002_f_at 7.339380 7.427014 7.114548 7.377403
1003_s_at 5.709777 6.663013 5.048440 4.982705
1004_at 7.722630 7.216481 7.337319 7.060342
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Exercise 6
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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.
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AffyBatch object
size of arrays=640x640 features (35221 kb)
cdf=HG_U95Av2 (12625 affyids)
number of samples=4
number of genes=12625
annotation=hgu95av2
notes=
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Model optimising ..........................
Expression values calculating ..........................
Done.
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20A 20B 10A 10B
100_g_at 6.001526 5.722812 5.815477 5.307755
1000_at 7.127891 7.079451 7.074755 6.822553
1001_at 4.647841 4.768898 4.076775 4.134697
1002_f_at 5.622159 5.522768 5.307126 5.423579
1003_s_at 1.640298 1.524951 1.961328 1.091461
1004_at 4.719888 4.156653 5.027276 4.164188
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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=
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Model optimising ..........................
Expression values calculating ..........................
Done.
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low10-1.cel low10-2.cel high10-1.cel high10-2.cel low48-1.cel
100_g_at 4.5636890 5.0542649 4.3147335 3.323781455 4.1293564
1000_at 7.0441500 6.7470287 6.1633587 6.023999895 5.9510488
1001_at -1.5355806 -1.4367264 -1.9746399 -0.097707515 1.1476384
1002_f_at -1.4571550 -0.9999348 -1.9062753 -1.185054088 -2.2071496
1003_s_at -2.0247799 -0.5052158 -0.1332393 0.889561658 0.6175251
1004_at 0.0781212 0.1790070 -0.3844425 -0.006124629 1.9511443
low48-2.cel high48-1.cel high48-2.cel
100_g_at 4.5447948 4.039069 4.1924974
1000_at 5.9870338 5.940411 5.6196507
1001_at -0.3794378 -2.924452 1.0317169
1002_f_at -1.9164036 -1.300294 -1.9311610
1003_s_at 2.0123121 1.550318 0.5264854
1004_at 1.3045113 2.029137 2.5490697
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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=
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Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘rma’ for signature ‘"AffyBatch"’
Traceback:
1. rma(affybatch.estrogen)
2. (function (classes, fdef, mtable)
. {
. methods <- .findInheritedMethods(classes, fdef, mtable)
. if (length(methods) == 1L)
. return(methods[[1L]])
. else if (length(methods) == 0L) {
. cnames <- paste0("\"", vapply(classes, as.character,
. ""), "\"", collapse = ", ")
. stop(gettextf("unable to find an inherited method for function %s for signature %s",
. sQuote(fdef@generic), sQuote(cnames)), domain = NA)
. }
. else stop("Internal error in finding inherited methods; didn't return a unique method",
. domain = NA)
. })(list(structure("AffyBatch", package = "affy")), structure(function (object,
. ...)
. standardGeneric("rma"), generic = structure("rma", package = "oligo"), package = "oligo", group = list(), valueClass = character(0), signature = "object", default = `\001NULL\001`, skeleton = (function (object,
. ...)
. stop("invalid call in method dispatch to 'rma' (no default method)",
. domain = NA))(object, ...), class = structure("standardGeneric", package = "methods")),
. <environment>)
3. stop(gettextf("unable to find an inherited method for function %s for signature %s",
. sQuote(fdef@generic), sQuote(cnames)), domain = NA)
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