GSEA on Cuffdiff log2(fold_change) values

adrian

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Join Date: Oct 2009

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GSEA on Cuffdiff log2(fold_change) values

09-08-2013, 06:44 PM

Hi:

I am using Cuffdiff log2(fold_change) values in 'rnk' file for GSEA.

Althought I had 8K genes, my C2_all set enrichment was only 1 gene set at FDR-25%.

My question is - is log2(fold_change) values - suitable for GSEA enrichment.

I mean - can I compare the AFfy log2 fold changes and cuffdiff log2(fold_change) values and do Pre-ranked enrichment.

Is the distribution meaningful for GSEA enrichment.

thanks
Adrian.
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