Hi,

I am trying to make a meta-anlaysis between microarray and RNA datasets. My aim is to generate normalized count matrix for each set. I try to use raw data when available and process them myself. However, I have to start from GEO Series Matrix for microarray data.

Microarray data pre-processed already as:

"The raw microarray data were processed by Lumi package in R, with background adjustment, variance-stabilizing transformation, and quantile normalization within each batch."

I believe this is a florescent signal normalization. I want to have the next step of normalization for DEG analysis with limma package. Yet, at that point I am confused where to start, which object to create etc. I need to process count matrix, not .CEL files.

Thanks in advance