User: alserg

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alserg390
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Posts by alserg

<prev • 32 results • page 1 of 4 • next >
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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 1 day ago by alserg390
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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 7 days ago by alserg390
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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 10 days ago by alserg390
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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 11 days ago by alserg390
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Answer: A: GSEA PreRanked lists from DESeq2 results table
... Definetly don't do adjusted P-values. Signed log (nominal) P-value or statistic (stat column) should be fine. I personally use the latter, but I don't have any arguments for this. From my experience the results are very similar. ...
written 13 days ago by alserg390
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Answer: A: fGSEA result to csv
... Use fwrite from data.table package: `fwrite(fgseaRes, file="fgsea.tsv", sep="\t", sep2=c("", " ", ""))` ...
written 11 weeks ago by alserg390
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Answer: A: Thousands of significant differentially expressed genes but no significant enric
... What value of nperm did you use for fgsea? Low values, like 1000, or sometimes even 10000 will limit the minial possible nominal P-value, which after BH-correction can lead to non-significant results. ...
written 12 weeks ago by alserg390
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Comment: C: Bonferroni multiple corrections question
... To clarify: fgsea adjusted P-values are Benjamini-Hochberg-adgjusted, not Bonferoni. ...
written 4 months ago by alserg390
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News: Bioinformatics Contest 2020. Call for problems
... This is a call for problems for the online Bioinformatics Contest 2020. We have been holding [the Contest](https://bioinf.me/en/contest) since 2017, and we hope to make it more diverse and international in the upcoming years. An important step in that direction for us is to ask the bioinformatics c ...
news contest written 5 months ago by alserg390
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Answer: A: Getting all gene members in a Reactome Pathway
... There is a package `reactome.db`: http://bioconductor.org/packages/release/data/annotation/html/reactome.db.html There you can select genes from reactome pathways. However, the IDs are not consistent with the online version, although pathway names are consistent. ...
written 7 months ago by alserg390

Latest awards to alserg

Appreciated 2 days ago, created a post with more than 5 votes. For Bioinformatics Contest 2020. Call for problems
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Bioinformatics Contest 2020. Call for problems
Teacher 6 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
Scholar 11 weeks ago, created an answer that has been accepted. For A: Is there a name for these charts?
Teacher 11 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
Scholar 23 months ago, created an answer that has been accepted. For A: Is there a name for these charts?
Teacher 23 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
Teacher 2.2 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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