User: a_liberzon

a_liberzon • 0

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Posts by a_liberzon

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Answer: A: How do you compare GSEA results between treatments?

... Another thought along the same lines. Once you have GSEA results as described above, you can compare ES (not NES) scores say, by a paired tTest for each of the enriched sets. ...

written 2.7 years ago by a_liberzon • 0

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Answer: A: How do you compare GSEA results between treatments?

... Why not trying two runs of standard (not pre-ranked) GSEA? Prepare a single GCT file with all your data, such that rows are probe set IDs, columns are samples for all perturbations (treatment A, treatment B and Controls). Next define a CLS file with the relevant 3 phenotype classes. Finally, run GSE ...

written 2.7 years ago by a_liberzon • 0

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Answer: A: Gene enrichment analysis with a simple gene list compared to microarray data

... Try our Investigate Gene Sets tool online at http://software.broadinstitute.org/gsea/msigdb/index.jsp Note that your list should not exceed 2,000 gene (or protein) identifiers, and that the online tool will only show up to 100 most significant results. If you have many lists like that, then I'd rec ...

written 2.7 years ago by a_liberzon • 0

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