bioconductor系列教程之二简单的Affymetrix 外显子(exon)分析流程（上）

教程数据下载并读入

下载数据需要你先注册一个帐号，然后再点击右上角的小logo下载。需要仔细地找一下。

下载解压后在同一文件夹下新建一个名为covdesc的文件，文件用tab间隔，内容如下：

	group
0306_YH148_EX_exMCF7_r1.CEL	a
0406_YH156_EX_exMCF7_r2.CEL	a
0406_YH157_EX_exMCF7_r3.CEL	a
0306_YH149_EX_exMCF10A_r1.CEL	b
0406_YH158_EX_exMCF10A_r2.CEL	b
0406_YH159_EX_exMCF10A_r3.CEL	b
0806_YH178_EX_100MCF7_r1.CEL	c
0806_YH179_EX_100MCF7_r2.CEL	c
0806_YH180_EX_100MCF7_r3.CEL	c
0806_YH181_EX_100MCF10A_r1.CEL	d
0806_YH182_EX_100MCF10A_r2.CEL	d
0806_YH183_EX_100MCF10A_r3.CEL	d

Ｒ中载入库文件：

> library(exonmap)
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: genefilter
Loading required package: RColorBrewer
Loading required package: RMySQL
Loading required package: DBI
> library("exon.pmcdf")

设置路径并读取文件

> setwd("~/Documents/exonArray/ExonarraysMCF7andMCF10Adata_cel")
> raw.data<-read.exon()
> raw.data@cdfName<-"exon.pmcdf"
> pData(raw.data)
                               sample group
0306_YH148_EX_exMCF7_r1.CEL         1     a
0406_YH156_EX_exMCF7_r2.CEL         2     a
0406_YH157_EX_exMCF7_r3.CEL         3     a
0306_YH149_EX_exMCF10A_r1.CEL       4     b
0406_YH158_EX_exMCF10A_r2.CEL       5     b
0406_YH159_EX_exMCF10A_r3.CEL       6     b
0806_YH178_EX_100MCF7_r1.CEL        7     c
0806_YH179_EX_100MCF7_r2.CEL        8     c
0806_YH180_EX_100MCF7_r3.CEL        9     c
0806_YH181_EX_100MCF10A_r1.CEL     10     d
0806_YH182_EX_100MCF10A_r2.CEL     11     d
0806_YH183_EX_100MCF10A_r3.CEL     12     d