User: assaron

gravatar for assaron
assaron140
Reputation:
140
Status:
Trusted
Location:
Twitter:
assaron
Last seen:
2 days ago
Joined:
2 years, 3 months ago
Email:
a********@gmail.com

Posts by assaron

<prev • 30 results • page 1 of 3 • next >
0
votes
2
answers
40
views
2
answers
Answer: A: Issues in generating workable rank file for GSEA
... Hi, In DESeq2 you can use t-statistic for ranking, there are no NA-s. If you still want to use p-values, set DESeq2 option cooksCutoff=FALSE for the results function. ...
written 2 days ago by assaron140
0
votes
0
answers
71
views
0
answers
Comment: C: ReactomePA / Reactome: GSEA error message
... Could you also paste the resul of any(duplicated(names(anaData)))? This is what is checked at fgsea. ...
written 2 days ago by assaron140
0
votes
2
answers
418
views
2
answers
Comment: C: Does fgsea order the stats argument?
... I guess, you can aggregate your values to get a new "statistic" that will be ordered as you want: e.g. stat=p+ifelse(p == 1, abs(effect) * 1e-3, 0).  Additionally, GSEA method were designed for statistics that can have both positive and negative values, so I suggest mutipltiplying the values by sig ...
written 3 months ago by assaron140
0
votes
1
answers
202
views
1
answers
Comment: C: BiocParallel: zombie processes on FORK cluster
... Indeed, it is fixed in R-devel. ...
written 5 months ago by assaron140
0
votes
1
answers
202
views
1
answers
Comment: C: BiocParallel: zombie processes on FORK cluster
... Thanks for the info! I'll try to check R-devel version ...
written 5 months ago by assaron140
3
votes
1
answer
202
views
1
answer
BiocParallel: zombie processes on FORK cluster
... Hello, Is it a knwon issue that bplapply function leaves zombie processes on FORK cluster? library(BiocParallel) b <- MulticoreParam(workers=4) bplapply(1:10, sqrt, BPPARAM=b) # here 4 zombie processes appear bplapply(1:10, sqrt, BPPARAM=b) # here another 4 zombie processes appear It could b ...
biocparallel parallel written 5 months ago by assaron140 • updated 5 months ago by Martin Morgan ♦♦ 21k
0
votes
1
answers
268
views
1
answers
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 8 months ago by assaron140
0
votes
2
answers
418
views
2
answers
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 10 months ago by assaron140
0
votes
1
answers
484
views
1
answers
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 10 months ago by assaron140
0
votes
1
answers
484
views
1
answers
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 10 months ago by assaron140

Latest awards to assaron

Scholar 11 months ago, created an answer that has been accepted. For A: Direction aware fgsea test
Scholar 2.3 years ago, created an answer that has been accepted. For A: Direction aware fgsea test
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: pre-ranked GSEA within R?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 296 users visited in the last hour