[BioC] converting probeset id to gene id's : fRMA

Abhishek Pratap abhishek.vit at gmail.com
Sat Jun 21 02:05:46 CEST 2014

Hey Guys

I am using fRMA to normalize n summarize some affy data. Post
normalization I am getting 54k uniq probe id's in the eSet.

I am wondering whats the best way to convert this expressionSet into a
gene level data. I thought fRMA's documentation said it would produce
gene level summarized values but I dont see that in the result. Can
fRMA do that or is there any other standard way of achieving this in

affyBatch_object <- ReadAffy(celfile.path=data_dir))
normData1 <- frma(affyBatch_object, summarize="random_effect")

appreciate any pointers.


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