[R] Creating One Single Object with Phenotype and Expression Data

[Martin Morgan]

Hey Ben -- this is a bioconductor question so please ask on the 
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Martin

On 10/07/2011 07:27 AM, Ben Ganzfried wrote:
> Hey,
>
> I have code that can check the quality of a data set we're working with
> (expression data), and I'm having some trouble writing code that would make
> the expression data we have tie to other data we want to link it to (called
> phenotype data).  Does anyone have any advice on how I could make a single
> object that would do this?  Other relevant info: I want to use the pdata()
> function, and I have all the phenotype data available as csv files.  Here is
> what I have in regards to the expression data:
>
> library(affy)
> library(arrayQualityMetrics)
>
> inputargs<- commandArgs(TRUE)
> print(inputargs)
> sessionInfo()
>
> strInputAccession<- inputargs[1]
> strBaseDir<- inputargs[2]
>
> processedDir<-
> paste(strBaseDir,strInputAccession,"PROCESSED/DEFAULT",sep="/")
> qcDir<- paste(strBaseDir,strInputAccession,"QC",sep="/")
> sampleFile<-
> paste(processedDir,"/",strInputAccession,"_RAWfilenames.txt",sep="")
> defaultExprs<-
> paste(processedDir,"/",strInputAccession,"_default_exprs.csv",sep="")
>
> if(file.exists(sampleFile)){
>    affyobj<- try(ReadAffy(filenames=read.table(sampleFile,as.is
> =T,header=FALSE)[,1]))
>    if(class(affyobj)=="try-error"){
>      rm(affyobj)
>    }else{
>      sampleNames(affyobj)<- sub("\\..*","",sampleNames(affyobj))  #get rid
> of .CEL etc extension, just keep GSM
>    }
> }
>
> if(!exists("affyobj")){
>    mdExprs<- as.matrix(read.csv(defaultExprs,row.names=1))
>    if( min( mdExprs, na.rm = TRUE )>= 0&  max( mdExprs, na.rm = TRUE )>= 50
> ) {
>      mdExprs<- log(mdExprs, base = 2) }
>    affyobj<- new("ExpressionSet",exprs=mdExprs)
> }
>
> x<- arrayQualityMetrics(expressionset = affyobj,
>                           outdir=qcDir,
>                           force = TRUE,
>                           spatial=FALSE)
>
> 	[[alternative HTML version deleted]]
>
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