{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [], "source": [ "options(jupyter.plot_mimetypes ='image/png')\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Step1" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [], "source": [ "setwd(\"~/Autumn2016/Week5/data_wk_5\")" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "'affybatch.estrogen'" ], "text/latex": [ "'affybatch.estrogen'" ], "text/markdown": [ "'affybatch.estrogen'" ], "text/plain": [ "[1] \"affybatch.estrogen\"" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stderr", "output_type": "stream", "text": [ "Loading required package: BiocGenerics\n", "Loading required package: parallel\n", "\n", "Attaching package: ‘BiocGenerics’\n", "\n", "The following objects are masked from ‘package:parallel’:\n", "\n", " clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n", " clusterExport, clusterMap, parApply, parCapply, parLapply,\n", " parLapplyLB, parRapply, parSapply, parSapplyLB\n", "\n", "The following objects are masked from ‘package:stats’:\n", "\n", " IQR, mad, xtabs\n", "\n", "The following objects are masked from ‘package:base’:\n", "\n", " anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,\n", " do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,\n", " intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget,\n", " order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,\n", " rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,\n", " union, unique, unlist, unsplit\n", "\n", "Loading required package: Biobase\n", "Welcome to Bioconductor\n", "\n", " Vignettes contain introductory material; view with\n", " 'browseVignettes()'. To cite Bioconductor, see\n", " 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n", "\n" ] } ], "source": [ "load(\"estrogen_data.RDA\")\n", "ls()\n", "library(affy)" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "AffyBatch object\n", "size of arrays=640x640 features (19 kb)\n", "cdf=HG_U95Av2 (12625 affyids)\n", "number of samples=8\n", "number of genes=12625\n", "annotation=hgu95av2\n", "notes=\n" ] } ], "source": [ "show(affybatch.estrogen)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Step 2" ] }, { "cell_type": "code", "execution_count": 21, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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 |