Hello,

I am trying to do a UPC normalization on a GEO dataset. Is there a way to produce read count files such that I can do the UPC normalization on all samples at once rather than each sample individually? I want to have one output file for the dataset. Is this possible?

Please let me know.

As stated in the documentation, you can specify multiple input files using the inFilePattern parameter of the UPC_RNASeq function. You would specify the input files using wildcard characters. Alternatively, you can put the data in an ExpressionSet object and process it using UPC_Generic_ExpressionSet.