User: alserg

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alserg520
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assaron
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Posts by alserg

<prev • 38 results • page 1 of 4 • next >
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Comment: C: fgsea nMoreExtreme meaning
... In the recent version `fgsea` has switched an algorithm that doesn't have `nperm` parameter. For compatibility reasons currently `fgsea` called with `nperm` parameter executes the old version, and without -- the new one. That's why you see a big difference in results. ...
written 9 weeks ago by alserg520
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Comment: C: fgsea nMoreExtreme meaning
... If you do, say 10k permutations and see `nMoreExtreme = 0`, that could mean you can't really tell, whether the nominal P-values is 1e-4, 1e-10 or 1e-100. Again, the optimal way is to update to the latest version of `fgsea`: there is no `nperm` parameter at all and arbitrarily low P-values can be e ...
written 9 weeks ago by alserg520
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Answer: A: fgsea nMoreExtreme meaning
... GSEA P-values are empirically calculated by sampling random gene sets. `nMoreExtreme` is indeed a number of times a random gene set had a more extreme enrichment score value and is used in nominal GSEA P-value calculation, which is equal `nMoreExtreme` normalized by number of random gene sets that h ...
written 9 weeks ago by alserg520 • updated 9 weeks ago by ATpoint36k
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Comment: C: GSEA on preranked list with weighted enrichment statistic (exponent=1) in R
... Actually, that's an important question. Broad GSEA recommendation for 0.25 is due to their ad-hoc correction procedure they developed because they didn't have enough accuracy for standard correction procedures. In fgsea we use standard Benjamini-Hochberg, so standard thresholds can be used. I even r ...
written 4 months ago by alserg520
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Comment: C: How to view all KEGG reactions?
... For example, like this: rxnrnz <- data.frame(rxn=names(rxn2enz), enz=rxn2enz) rxn2enz <- data.frame(rxn=names(rxn2enz), enz=rxn2enz) enz2hsa <- data.frame(enz=names(enz2hsa), hsa=enz2hsa) ...
written 5 months ago by alserg520
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Comment: C: GSEA PreRanked lists from DESeq2 results table
... Yes, changing Inf to a big number should work fine. ...
written 5 months ago by alserg520
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Comment: C: Bioinformatics Contest 2020. Call for problems
... We haven't been able to gather a good problem set for this year, so the contest is put off till 2021. The call for problems is still active. ...
written 5 months ago by alserg520
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Answer: A: GSEA after MACS2 peak calling for ChIP-seq; want positive enrichment only
... Development version of fgsea (from github) supports one-tailed tests. However, we don't see much of a difference compared to a standard approach. See here in more details: https://github.com/ctlab/fgsea/issues/27 ...
written 6 months ago by alserg520
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Comment: C: GSEA PreRanked lists from DESeq2 results table
... I'm not that familiar with edgeR pipeline. Isn't F-statistic a positive one, not signed? If so, it's a shady territory. The method will work: it will say whether or not gene set look uniformly distributed, but you should be careful with the interpretation. In any case, don't remove gene based on st ...
written 6 months ago by alserg520
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Comment: C: GSEA PreRanked lists from DESeq2 results table
... Usually, there is no P-value of exactly one. But as I said, I prefer using the statistic, which is very straightforward. ...
written 6 months ago by alserg520

Latest awards to alserg

Scholar 9 weeks ago, created an answer that has been accepted. For A: Is there a name for these charts?
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: fGSEA result to csv
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: fgsea nMoreExtreme meaning
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler
Appreciated 3 months ago, created a post with more than 5 votes. For Bioinformatics Contest 2020. Call for problems
Scholar 4 months ago, created an answer that has been accepted. For A: Is there a name for these charts?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler
Appreciated 5 months ago, created a post with more than 5 votes. For Bioinformatics Contest 2020. Call for problems
Popular Question 7 months ago, created a question with more than 1,000 views. For Bioinformatics Contest 2020. Call for problems
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler
Scholar 8 months ago, created an answer that has been accepted. For A: Is there a name for these charts?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler
Scholar 2.4 years ago, created an answer that has been accepted. For A: Is there a name for these charts?
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler

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