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Converting multiple GSE data into expression matrix

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.

r wgcna deg expression matrix
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written by ghataksoumyakanti • ghataksoumyakanti

1 answer

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

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