Hi, I'm a research assistant in a cancer lab and I'm trying to make a single object that will link our expression data with its associated phenotype data. I want to use the pdata() function and I have all the phenotype data available as csv files. I'm a little confused about the best approach to make this single object and would greatly appreciate any advice you may have. Here is the script generating expression values that I want to add the code to: 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) [[alternative HTML version deleted]]