User: krassowski.michal

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Posts by krassowski.michal

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Limma linear fit residual standard deviation calculation
... 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 ...
limma written 5 hours ago by krassowski.michal0 • updated 1 hour ago by Gordon Smyth38k
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Answer: A: PLAGE method fails in GSVA if an overlap between gene sets and genes in expressi
... 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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PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
... 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 ...

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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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