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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 getInfo() function.

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?

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Finally, I found it. filelist.txt file is accessible from the FTP server of the NCBI. For example for that specific microarray is stored here

So there might be a problem at software side and they don't get downloaded.

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  • $\begingroup$ I know you now solved the issue, but I think you should double check the real manual of GEOquery. But I think that the problem is with the type of data that is provided, I recall having downloaded this file with getGEOSuppFile $\endgroup$
    – llrs
    Commented Feb 27, 2018 at 20:50

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