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  • adrian
    Member
    • Oct 2009
    • 90
    #1

    GSEA on Cuffdiff log2(fold_change) values

    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.
    Tags: None
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