Converting multiple GSE data into expression matrix

Question

[ghataksoumyakanti]

Hi guys,I have downloaded 4 GSE microarray datasets from geo with their cel files and their individual series expression matrix.My furthur intention is to do a weighted gene coexpression analysis on the combined data or the DEGs I got from those GSE files.Should I combine the 4 expression matrix togetehr and then do a WGCNA analysis or should I find the DEGs from all 4 GSE datasets and do WGCNA on them.

In either case can someone tell me the process to do so. Thanks in advance.

Answer 1

[Satyajeet Khare]

1. Create a Gene level expression matrix by combining probe IDs.
2. Remove batch effect (e.g. using limma).
3. Use for WGCNA

[ghataksoumyakanti]

Can u please elaborate point 1...