Expression data file

[Nishi]

Hi,

I read the previous conversation on the Expression Dataset but I'm still confused as to what "counts" are used in the expression data file. 

I understand that I have to use the normalised data, so after running the different expression analysis, but which values should I use for the expression file? Would it be the logCPM that has been normalised using TMM? 

Thank you! 

[Anthony Castanza]

Our standard recommendation is for a DESeq2 based method where an internal "normalized count" table is extracted from the DESeq2 object. One reason for this recommendation is that this output is made available by the "standard" implementations of DESeq2 through Galaxy or GenePattern, and is therefore relatively easy to obtain as an acceptable input. However, TMM-normalized logCPM should also be an acceptable method for normalization of expression data for GSEA.

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

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[Nishi]

Thanks for clarifying!