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)

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