gsva on custome annotation

Question

[colonppg]

I have a general question on how to use nsfilter before running gsva, the answer is probably some where but I have not find it, the situation is:

I am working with affy exon array, to run gsva: 1. I made the probe level summary for each gene 2. I then constructed the eset

however, running nsfilter has a lot of issue, because I am not sure how under the hood nsfilter works, how does the program know what I am filter on?

by the way, my gene list for gsva is gene symbols, how it maps to the annotation to the custome annotation file has been a mystery to me...

the program works fine for standard arrays but it always has been a headache when running on unconventional platforms, any help is appreciated here...

Thanks