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Hi,
I have been trying to use UPC_Generic_ExpressionSet function from the SCAN UPC package with Human Exon Array dataset and was stuck at a point. I want to use UPC based detection and correct for GC content but the sequence file for Affymetrix is at probe level whereas I am using alternative exon array mappings from BrainArray. Thus the expressionset contains SCAN normalised intensities at exon level. In this case do I need to supply information about sequence of each exon? If not then how should I approach this when using alternate mappings?
Thanks.
Thanks for the reply. When I used the UPC detection function with the Affymetrix platform the function runs through the iterations but each time it shows No correction will be made for GC content. That confused me a bit but I think that is probably because no argument is passed to the sequenceFeatureName.
The output doesn't say that specifically, but it should be doing it. If you want, you can send me the code you are using, along with the output, and I can take a look.