User: krassowski.michal

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Posts by krassowski.michal

<prev • 3 results • page 1 of 1 • next >
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... This is a low-level question, but I am very curious about the reason for limma calculating the residual standard deviation (sigma) in lmFit (or more precisely, lm.series) as:  # 1. lm.series sqrt(mean(out$effects[-(1:out$rank)]^2))  rather than: ` # 2. what I would expect x <- out ...
written 5 hours ago by krassowski.michal0 • updated 1 hour ago by Gordon Smyth38k
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... I hypothesized that the gene sets with overlap of one are the issue; I tried another such one - for entrez ids limited to 1000 one of such gene sets is KEGG_GALACTOSE_METABOLISM and the problem appeared again. Then I filtered out all gene sets with overlap lower than two and tried to run my program ...
written 6 months ago by krassowski.michal0
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... I've been using GSVA with three methods: gsva, ssgsea and z-score for some time now, with success and without problems. However, when I tried to use the forth method - PLAGE - I found out that it does not work with some of the gene sets. Specifically I've discovered that using MSigDB Kegg collection ...
written 6 months ago by krassowski.michal0

Latest awards to krassowski.michal

Scholar 6 months ago, created an answer that has been accepted. For A: PLAGE method fails in GSVA if an overlap between gene sets and genes in expressi

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