Question: Converting multiple GSE data into expression matrix
0
gravatar for ghataksoumyakanti
3 months ago by
ghataksoumyakanti0 wrote:

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.

wgcna deg expression matrix R • 256 views
ADD COMMENTlink written 3 months ago by ghataksoumyakanti0
0
gravatar for Satyajeet Khare
3 months ago by
Satyajeet Khare1.5k
Pune, India
Satyajeet Khare1.5k wrote:
  1. Create a Gene level expression matrix by combining probe IDs.
  2. Remove batch effect (e.g. using limma).
  3. Use for WGCNA
ADD COMMENTlink modified 3 months ago • written 3 months ago by Satyajeet Khare1.5k

Can u please elaborate point 1...

ADD REPLYlink written 3 months ago by ghataksoumyakanti0
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