Basic Problem: When I analyse microarray data (Treated vs. Control) with GEO2R I get some 1000 genes above lfc=1 but when I do that analysis by using either GCRMA or RMA and then limma I get only 3 genes above lfc=1.
I want to do differential gene expression analysis of multiple drug vs. treated cases. I was wondering if it is possible to read the cel files but instead of using RMA or GCRMA use the log-transformation as is done by GEO2R. I am encountering problem in making an expression-set by reading the cel files without using RMA and GCRMA.
If somebody has tried it this way then share your experience. Thanks.
Note: The dataset I have doesn't contains series matrix file, otherwise I could have use GEO2R approach simply. So only thing I have is cel files.