How to obtain normals-subtracted tumor data

[Oğuzhan]

Hi Anthony,

Is it possible to compare the enriched gene sets between tumor and their corresponding matched normal samples to obtain normals-subtracted tumor data. Because in my analysis there is 4 groups. Tumor, matched normal, recurrent tumor and matched normal. Intrestingly, when I compare the the matched normals I find the highest enriched gene set number. I think nothing should be different between these two control groups. Am I wrong? But if I had the option to first compare the tumor and matched normals, and obtain the normals-subtracted tumor data, next to compare normals-subtracted tumor data between these two groups it would be better. Do you have any suggestion for this comparision.
All the best,
Oğuzhan

[Castanza, Anthony]

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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