On my way to create a co-expression matrix for a microarray experiment, using the
coexnet package I had to use a function called
getAffy() which according to the packages' manual it :
searches in your current or designated path file the folder with the GSE accession number and reads the filelist.txt file that contains the name of each GSM sample, in order to recognize them and join them in an unified AffyBatch object.
So in some way, this file is needed to create the AffyBatch object. The thing here is that there is no such a file downloaded from the
Googling out the
filelist.txt I reached only this result from GEOQuery manual, referring to that file. And as you can see there is a command in it
eList2 <- getGEOSuppFiles("GSE11675") that is believed that it returns also the filelist.txt. I tried even with the example of the previously mentioned command, but no filelist.txt file ever fetched.
Is there any way to setup my own filelist.txt file? Does anyone know what it contains and in what form?