User: assaron

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assaron130
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assaron
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Posts by assaron

<prev • 24 results • page 1 of 3 • next >
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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 weeks ago by assaron130
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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 12 weeks ago by assaron130
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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 3 months ago by assaron130
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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 3 months ago by assaron130
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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 3 months ago by assaron130
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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 4 months ago by assaron130
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Comment: C: Does fgsea order the stats argument?
... Can you provide an example where it's useful? ...
written 5 months ago by assaron130
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Answer: A: Does fgsea order the stats argument?
... Yes, it does sort stats argument. Sorting stats values is inherent to pre-ranked gsea. Is it really what you want to do? ...
written 5 months ago by assaron130
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Comment: C: Change in pathway IDs scheme in reactome.db
... Can you check with Valerie?  It'd be better with new version number, because it would be easier to check if it was updated or not. ...
written 7 months ago by assaron130
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Comment: C: Change in pathway IDs scheme in reactome.db
... I still can't see the updated version in Bioconductor. Is this OK? There are still 2185 PATHID's in the packge. Also, should the reactome.db version change with this update, from 1.59.0 to 1.59.1 or something? ...
written 7 months ago by assaron130

Latest awards to assaron

Scholar 20 months ago, created an answer that has been accepted. For A: Direction aware fgsea test
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: pre-ranked GSEA within R?

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