Hi-- apologies if this is a duplicate email.  I just joined the list today
and I didn't know how long the email I just sent before I joined would be
under moderator approval.

As a brief introduction, I'm a research assistant in a cancer lab.  I
graduated from college in 2009 and didn't see myself getting involved in
medical research at all until I served as a bone marrow donor for my brother
a year ago.  I'm currently finishing up classes to go to medical school and
I work in a bioinformatics lab where I'm really enjoying learning how to use
R through fun projects.

My current project requires me to make a single object that will link our
expression data with its associated phenotype data, and I'm a little
confused about the best approach to do this.  I want to use the pdata()
function and I have all the phenotype data available as csv files, and I
would greatly appreciate any specific advice you may have about how to
implement this.  Here is the script so far that generates expression values,
and I want to add the single object to this ideally:

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)
}

#I'd like to make one single object with phenotype and expression data here


x <- arrayQualityMetrics(expressionset = affyobj,
                         outdir=qcDir,
                         force = TRUE,
                         spatial=FALSE)

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