R help - Oct 2011 - Creating One Single Object with Phenotype and Expression Data

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]]

Hey Ben -- this is a bioconductor question so please ask on the 
Bioconductor mailing list. Good news, you don't have to subscribe to post

http://bioconductor.org/help/mailing-list/

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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