User: assaron

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assaron100
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assaron
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Posts by assaron

<prev • 20 results • page 1 of 2 • next >
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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 1 hour ago by assaron100
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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 days ago by assaron100
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Comment: C: Does fgsea order the stats argument?
... Can you provide an example where it's useful? ...
written 4 weeks ago by assaron100
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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 4 weeks ago by assaron100
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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 3 months ago by assaron100
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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 3 months ago by assaron100
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Comment: C: Change in pathway IDs scheme in reactome.db
... I'd wait with updates for after the release. It seems that even the updated version is not propagated yet. On Fri, Apr 21, 2017, 15:57 willem.ligtenberg [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User willem.ligte ...
written 3 months ago by assaron100
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Comment: C: Change in pathway IDs scheme in reactome.db
... Oh, I see. Yes, it does. ...
written 3 months ago by assaron100
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Comment: C: Change in pathway IDs scheme in reactome.db
... When it should be available at bioconductor 3.5? It's a release date soon... ...
written 3 months ago by assaron100
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Comment: C: Change in pathway IDs scheme in reactome.db
... I see. Well, as you say, the package just reflects reactome database, so I'd argue it's better to have ids consistent with current reactome ids, that is of the form like R-HSA-<ID>. Btw, did I got it right that there is a new version coming very soon with unique ids?   ...
written 3 months ago by assaron100

Latest awards to assaron

Scholar 16 months ago, created an answer that has been accepted. For A: Direction aware fgsea test
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: pre-ranked GSEA within R?

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