Hi Oğuzhan,
That is odd, I would wonder if there is some batch effect or other confounding variable in your data. Perhaps check your normalization methodology.
That said, yes, you can perform GSEA with the control-normalized data, In our user guide we suggest that the “cosine” ranking metric might be appropriate:
● Cosine is a variant of Pearson’s that is defined by Eisen et al. (1998). It is appropriate only when the expression profiles are based on log-expression ratios relative to a control.
https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm#_Metrics_for_Ranking
Let me know if you have more questions!
-Anthony
Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Department of Medicine
University of California, San Diego
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