Dear all, I have read cel files from ncbi website using the getGEO from GEOquery package. I want then to use the combineaffybatch from the matchprobe package but the objects I have to pass is affybatch. I need to convert the gse object or the expression sets to affybatch to be able to use it. Any ideas? Regards,salwa [[alternative HTML version deleted]]

On Thu, Feb 9, 2012 at 2:35 PM, Salwa Eid <salwaeid at="" hotmail.com=""> wrote: > > > > > Dear all, ? ?I have read cel files from ncbi website using the getGEO from GEOquery package. ?I want then to use the combineaffybatch from the matchprobe package but the objects I have to pass is affybatch. ?I need to convert the gse object or the expression sets to affybatch to be able to use it. ?Any ideas? Regards,salwa > Hi, Salwa. You cannot convert a GSE object or ExpressionSet into an affybatch since the probe-level data are not contained in either object. The getGEO function downloads the normalized data from GEO, not the .CEL files. You want to use the getGEOSuppFiles() function instead. This will download raw data, typically in .tar format. You can use the untar() function to then expand the archive. Finally, you can use the affy package to read the .CEL.gz files to get an affybatch. Hope that helps. Sean