I'm planning to run a GSE Analysis on some microarray datasets. Until now what I have done is to pre-processed them using frma algorithm.
The reason I chose frma instead of gcrma or rma is that I wanted to merge these different dataset into one.
Here is how I'm planing to proceed:
dataset1 : 3x Controls , 3x Treatment1
dataset2 : 2x Controls , 2x Treatment2
dataset3 : 2x Controls , 2x Treatment3
7x Controls , 3x Treatment1 , 2x Treatment2 , 2x Treatment3
Then I will execute the GSEA for controls , Treatmen1 , Treatment2 and Treatment3 separably.
So the question is if it's more reasonable to follow the path that I described or to run the GSEA on the separate datasets (for example for each control ) and then get the intersect of the gene sets of these three repetitions.