User: assaron

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assaron100
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assaron
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Posts by assaron

<prev • 16 results • page 1 of 2 • next >
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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 4 weeks 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 5 weeks 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 5 weeks ago by assaron100
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Comment: C: Change in pathway IDs scheme in reactome.db
... Oh, I see. Yes, it does. ...
written 5 weeks 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 5 weeks 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 5 weeks ago by assaron100
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Comment: C: Change in pathway IDs scheme in reactome.db
... I think the form  R-<three letter abbreviation species>-<number> is good enough. Not sure why would anyone want the ids to be numeric only.  ...
written 5 weeks ago by assaron100
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Change in pathway IDs scheme in reactome.db
... I just found out that in recent reactome.db version (1.59.0) there was a change of pathways IDs (PATHID column). Before there was 20800 pathways with pathways beeing specific to an organism. Now there are 2185 pathways, shared between organisms. I'm not sure what were the reasons for the change, but ...
reactome.db fgsea written 5 weeks ago by assaron100 • updated 5 weeks ago by willem.ligtenberg130
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Comment: C: Statistic for GSA
... fgsea works downstream of gene ranking, so it's impossible to do sample permutations and only gene permutations are used for the test. ...
written 3 months ago by assaron100
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Answer: A: Direction aware fgsea test
... Hi,  The GSEA test is itself directional, so you don't need to invert sign yourself. There are pathways with positive and negative enrichment scores (ES or NES). May be the example that goes with fgsea is not the best one, as the top-regulated pathways go in the same direction, but still there are ...
written 4 months ago by assaron100

Latest awards to assaron

Scholar 14 months ago, created an answer that has been accepted. For A: Direction aware fgsea test
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: pre-ranked GSEA within R?

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