User: assaron

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assaron150
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assaron
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Posts by assaron

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Comment: C: GSEA for RNA-seq analysis
... Gordon, could you, please, provide one or two links about p-value correction methods being incompatible with permutation tests? It'd love to read more about it. ...
written 10 days ago by assaron150
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Comment: C: GSEA for RNA-seq analysis
... 1. Actually, some time ago I implemented label-permuting GSEA test in fgsea package with a difference of calculating adjusted p-values with BH method, as opposed to ad-hoc NES-based method in Broad's version, and it turned out to be too conservative: I couldn't find a dataset where there were any si ...
written 9 weeks ago by assaron150
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Comment: C: fgsea p-values are mostly the same upon analysis
... First, having exactly the same low p-values is normal for fgsea as the algorithm is based on empirical sampling, so there is a minimal possible p-value. I would guess that here you used nperm=10000, hence 1e-4 p-values. What's strange is high p-values for hign NES values (1.7e-2 and 3.06 for Transl ...
written 3 months ago by assaron150
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Answer: A: Issues in generating workable rank file for GSEA
... Hi, In DESeq2 you can use t-statistic for ranking, there are no NA-s. If you still want to use p-values, set DESeq2 option cooksCutoff=FALSE for the results function. ...
written 4 months ago by assaron150
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Comment: C: ReactomePA / Reactome: GSEA error message
... Could you also paste the resul of any(duplicated(names(anaData)))? This is what is checked at fgsea. ...
written 4 months ago by assaron150
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Comment: C: Does fgsea order the stats argument?
... I guess, you can aggregate your values to get a new "statistic" that will be ordered as you want: e.g. stat=p+ifelse(p == 1, abs(effect) * 1e-3, 0).  Additionally, GSEA method were designed for statistics that can have both positive and negative values, so I suggest mutipltiplying the values by sig ...
written 7 months ago by assaron150
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Comment: C: BiocParallel: zombie processes on FORK cluster
... Indeed, it is fixed in R-devel. ...
written 9 months ago by assaron150
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Comment: C: BiocParallel: zombie processes on FORK cluster
... Thanks for the info! I'll try to check R-devel version ...
written 9 months ago by assaron150
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BiocParallel: zombie processes on FORK cluster
... Hello, Is it a knwon issue that bplapply function leaves zombie processes on FORK cluster? library(BiocParallel) b <- MulticoreParam(workers=4) bplapply(1:10, sqrt, BPPARAM=b) # here 4 zombie processes appear bplapply(1:10, sqrt, BPPARAM=b) # here another 4 zombie processes appear It could b ...
biocparallel parallel written 9 months ago by assaron150 • updated 9 months ago by Martin Morgan ♦♦ 22k
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Answer: A: GSEA using clusterprofileR
... clusterProfiler/fgsea differs from Broad GSEA in the multiple-hypotheses correction procedures. The latter uses an ad-hoc procedure while the former uses any standard method with Benjamini-Hochberg being the default one. I would recommend using at least 10000 permuations for  clusterProfiler/fgsea ( ...
written 12 months ago by assaron150

Latest awards to assaron

Scholar 15 months ago, created an answer that has been accepted. For A: Direction aware fgsea test
Scholar 2.6 years ago, created an answer that has been accepted. For A: Direction aware fgsea test
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: pre-ranked GSEA within R?

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