Bioconductor基因芯片數(shù)據(jù)分析系列(一)：數(shù)據(jù)的讀取

1、Bioconductor基因芯片數(shù)據(jù)分析系列（一）：R包中數(shù)據(jù)的讀取R軟件的Bioconductor包是分析芯片數(shù)據(jù)的神器，今天小編打算推出芯片數(shù)據(jù) 的系列教程。首先講數(shù)據(jù)讀取，以 CLL數(shù)據(jù)包中的數(shù)據(jù)為例。打開 R studio。#安裝所需的R包以及CLL包，注意大小寫，一般函數(shù)都是小寫的source("http:/biocLite.R");biocLite( CLL')0 O 0RStudio-Lh & e)i13一行.1Source 3nlConsole 7 0®P IJf I.個(gè)F n寓 +，I *RJ&am

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5、4.0 ?bic)Jit白 for help圖1.顯示已經(jīng)安裝好Bioconductor 了，版本為3.4#打開CLL包 library(CLL)而 0 (",RStudio更L. Wt . I 向 S I i /匚口 h 口 工SourceConsote 7 r G1EiF1> libraryCO.O affy 敕人雷要的理將色：BiocGcnerics 里人需要的雇霸包二pn rail lei現(xiàn)人招輯包, EiQcGenui"ix5"rne following ot>j ects ere niasKed from * package :por an

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9、; cttatlon(；*pKgnafnehhj',圖2.顯示打開CLL成功圖3.右側(cè)欄內(nèi)可見看到目前載入的程序包data(CLLbatch)# 調(diào)用RMA算法對(duì)數(shù)據(jù)預(yù)處理CLLrma<-rma(CLLbatch)# 讀取處理后所有樣品的基因表達(dá)值 e<- exprs(CLLrma)# 查看數(shù)據(jù)e我們可以看到，CLL數(shù)據(jù)集中共有24個(gè)樣品(CLL10.CEL, CLL11.CEL, CLL12.CEL, 等)，此數(shù)據(jù)集的病人分為兩組：穩(wěn)定組和進(jìn)展組，采用的設(shè)計(jì)為兩組之間的對(duì) 照試驗(yàn)(Control Test)。從上面的結(jié)果可知，Bioconductor具有強(qiáng)大的數(shù)據(jù)預(yù)處 理

10、能力和調(diào)用能力，僅僅用了 6行代碼就完成了數(shù)據(jù)的讀取及預(yù)處理。Bioconductor基因芯片數(shù)據(jù)分析系列（二）：GEO下載數(shù)據(jù)CEL的讀取ge心 為二祀dUtr.sq 產(chǎn)陰.同亙 Eman we。GEOOne EMartJiMn ")打型)us登陸pubmed ,找到一個(gè)你感興趣的數(shù)據(jù)庫首先得下載一個(gè)數(shù)據(jù)，讀取 GEO的CEL文件采用如下命令:CcunirvScuth KorflahJCBI 工 EEO > Afeeuinn Display U5c x: seif fj Formats html i Arrount; ourik 0G&D aecessiori：后正3

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15、ms (13GLlOSSS IkimurH HumanMTrN V4 0 也內(nèi)，“on bdddh pCSM 明 01?R5617(335061 HGSM890129GSMsgonoPHJNA153255Flla type/ruaurcfii2&.2 Mb TOPLCUStam TAR125,9 M3 ftcXhrtp)NUM N1H GK) 5 口苦C3imer AccessIb lity5617B35061J5617035061_LRationsBio ProjectGSE3B376 n on - mo rm al ized: Htxt agz代后 向tm 店 avails&

16、;fc 8 Sene5 reeBProceed Mg WAMT的的內(nèi) 防小用戶用加eWaEpf !：433J H More.,.Suotrtnnwn 理RA啊tar|Analyrze with GEO2RDownload familySOFT formifUud r*mlly nie(v)MINiHL formaftEd famly Hte(s)Seri ess. Matrix File(s)FormatSOFT ffi 下載 M1MML IM* TYTlflQuery DaiaiSets fcr GSE3£376Series G&E36376% NCBIHOVE 5EARC

17、-*在底下欄目下載CEL文件打開 R 軟件#安裝所需的R 包以及 CLL 包，注意大小寫，一般函數(shù)都是小寫的source("/biocLite.R"); biocLite( “CLL”)>library(affy)>affybatch<- ReadAffy(celfile.path = "GSE36376_RAW")請(qǐng)注意目錄的路徑，在window 下，反斜杠 要用轉(zhuǎn)義字符“ ”表示。然后可以使用RMA或者M(jìn)AS5等方法對(duì)數(shù)據(jù)進(jìn)行background.correction, normalizt

18、ion, pm.correct 等等一系列處理。如果你一切用默認(rèn)參數(shù)，則可以使用如下命令：>eset<- rma(affybatch) ， or eset<- mas5(affybatch)>exp<- exprs(eset)exp 就是數(shù)字化的表達(dá)譜矩陣了請(qǐng)注意，rma只使用匹配探針(PM)信號(hào)，exp數(shù)據(jù)已經(jīng)進(jìn)行l(wèi)og2處理。mas5 綜合考慮PM和錯(cuò)配探針(MM)信號(hào)，exp數(shù)據(jù)沒有取對(duì)數(shù)。下一期就得等到2017 年春節(jié)期間啦，敬請(qǐng)期待另外一種是直接利用 GEO上面的GEO2R按鈕里面的R script下載文件：# Version info: R 3.2.3

19、, Biobase 2.30.0, GEOquery 2.40.0, limma 3.26.8# R scripts generated Mon Dec 26 06:54:42 EST 2016Server: Query:acc=GSE36376&platform=GPL10558&type=txt&groups=&colors=&selection=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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