AudreyKauffmann,WolfgangHuber
January26,2008
Loadtherequiredpackages
>library(\"Biobase\")>library(\"limma\")>library(\"CCl4\")
ReadthedataandconvertthemintoanRGList
TheGenepix(.gpr)datafilesareintheextdatadirectoryoftheCCl4package.Ifyouhavethepackageinstalled,wecanlocatethemonyourfilesystemwiththefunctionsystem.file.Ifthefilesaresomewhereelse,pleaseadaptthebelowassignmenttodatapath.>datapath=system.file(\"extdata\package=\"CCl4\")
>p=read.AnnotatedDataFrame(\"samplesInfo.txt\path=datapath)>CCl4_RGList=read.maimages(files=sampleNames(p),+path=datapath,+source=\"genepix\+columns=list(R=\"F635Median\Rb=\"B635Median\+G=\"F532Median\Gb=\"B532Median\"))
Ifthiscodeisrunintheinst/docdirectoryoftheCCl4(source)package,theoutputdatafileswillbewrittendirectlyintothedatadirectoryofthepackage.Otherwise,justwriteintoatemporarydirectory.
>outdir=file.path(\"..\\"..\\"data\")>if(!isTRUE(file.info(outdir)$isdir))+outdir=tempdir()
>save(CCl4_RGList,file=file.path(outdir,\"CCl4_RGList.RData\"))
Thefunctionread.maimagesfromthelimmapackagereadsthe.gprfilesandbuildsanRGListobjectfromit.
Theoutputiswrittento>outdir
[1]\"../../data\"
BuildanNChannelSetfromtheRGList
OncetheRGListobjecthasbeencreated,wecanbuildanNChannelSet.
1
>sessionInfo()
Rversion2.6.1(2007-11-26)x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_Uattachedbasepackages:[1]toolsstatsgraphics[8]base
otherattachedpackages:[1]CCl4_1.0.7limma_2.12.0
grDevicesutilsdatasetsmethods
Biobase_1.16.2
Table1:TheoutputofsessionInfoonthebuildsystemafterrunningthisvignette.>>>+>+++>
featureData=new(\"AnnotatedDataFrame\data=CCl4_RGList$genes)assayData=with(CCl4_RGList,assayDataNew(R=R,G=G,Rb=Rb,Gb=Gb))varMetadata(p)$channel=factor(c(\"G\\"R\\"G\\"R\"),
levels=c(ls(assayData),\"_ALL_\"))
CCl4<-new(\"NChannelSet\
assayData=assayData,
featureData=featureData,phenoData=p)
save(CCl4,file=file.path(outdir,\"CCl4.RData\"))
2
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