I have to perform differential gene expression analysis using
limma. Can I use GEO Series Matrix File(s) (expression set) in the limma workflow (differential expression analysis) without actually extracting the expression set from raw
.CEL files. As I can see that
limma workflow involves
rma() correction before extraction of expression set but I can't find any information that states whether the GEO Series Matrix File(s) (expression set) is pre-processed or not.