User: assaron

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assaron140
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assaron
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Posts by assaron

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Comment: C: BiocParallel: zombie processes on FORK cluster
... Indeed, it is fixed in R-devel. ...
written 6 weeks ago by assaron140
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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 6 weeks ago by assaron140
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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 6 weeks ago by assaron140 • updated 6 weeks ago by Martin Morgan ♦♦ 21k
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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 4 months ago by assaron140
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Comment: C: Does fgsea order the stats argument?
... Sorry, I still don't understand. You can only sort something by one value, how can you sort first by p-value and then by effect size? I usually rank (and sort) genes by statistic from DE test (DESeq2 or limma), I know other people sort by log(p-value) * sign(log2FC). Both variants works fine and ac ...
written 6 months ago by assaron140
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Comment: C: FGSEA only runs with <1000 permutations
... One more thing: you can try to ask a question directly about BiocParallel package. Probably its maintainers will be able to give an answer. ...
written 6 months ago by assaron140
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Comment: C: FGSEA only runs with <1000 permutations
... Not really sure how to deal with this. Can you try other parallel backend, for example running bplapply(1:10, sqrt, BPPARAM = SnowParam())? If it works, you can set BPPARAM option for fgsea.   Additionally, I would check that mclapply works by running mclapply(1:10, sqrt). ...
written 6 months ago by assaron140
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Answer: A: FGSEA only runs with <1000 permutations
... Can you check that BiocParallel package works? For example run: library(BiocParallel) example("bplapply") It should finish withing seconds. ...
written 7 months ago by assaron140
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Answer: A: Retrieve the reactome ID of a protein
... I believe this information is not present in reactome.db package. You can try to check raw simplified reactome databse: http://reactome.org/pages/documentation/developer-guide/simplified-database/ There is a table with external identifiers.  ...
written 7 months ago by assaron140
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Comment: C: Does fgsea order the stats argument?
... Can you provide an example where it's useful? ...
written 8 months ago by assaron140

Latest awards to assaron

Scholar 23 months ago, created an answer that has been accepted. For A: Direction aware fgsea test
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: pre-ranked GSEA within R?

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