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]]
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
