User: idomtamir

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idomtamir10
Reputation:
10
Status:
New User
Location:
Austria
Last seen:
9 months ago
Joined:
3 years, 1 month ago
Email:
i********@gmail.com

Posts by idomtamir

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Looking for packages for SPR or BLI data analysis
... Did you find anything? ...
written 14 months ago by idomtamir10
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Comment: C: .onLoad failed in loadNamespace() for 'BiocInstaller'
... Thanks! the option(useHTTPS=FALSE) in my knitr driver script works. Wierd though, because it worked without it for a long time. ...
written 23 months ago by idomtamir10
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.onLoad failed in loadNamespace() for 'BiocInstaller'
... Something has changed in my setup and now I have a problem running an old knitr analysis and I cant load vsn anymore within the Rnw file, but I can load it the same R session, script etc ... and then every script (also knitr) analysis runs without problems. R session: >knit("report.Rnw", "test ...
software error knitr written 23 months ago by idomtamir10 • updated 23 months ago by Martin Morgan ♦♦ 21k
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Comment: C: mm10 ENSEMBL not available for GOSEQ
... I missed that it did work with mm10 once which is very strange. I just installed it fresh and it did not work with mm10 and ensGene. I don't think reinstalling will help you.   ...
written 3.0 years ago by idomtamir10
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Answer: A: mm10 ENSEMBL not available for GOSEQ
... These are just warnings. The problem is that goseq has to be always updated with new builds and the maintainers don't seem to do this. Seems like you have to do this yourself. https://support.bioconductor.org/p/55649/ Maybe community could take iover to add gene length info to the database. I als ...
written 3.0 years ago by idomtamir10
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GoSeq: Wallenius 264 overrepresented sampling 0?
... Hi, I use goseq and with the Wallenius approximation I get 264 BH adjusted significant overrepresented categories, with the sampling (1000 rep) I get 0 at a cutoff of 0.05. I should be reasonable, sincere and always use resampling and if theres nothing then that's the result - right?   ...
goseq written 3.0 years ago by idomtamir10 • updated 3.0 years ago by Gordon Smyth33k
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GoSeq: use ENSEMBLTRANS as input
... Hi, I am thinking about switching from GoStats to GoSeq. Is there a built in possibility to use the ENSEMBL transcript annotation or can I only use ENSEMBL genes? Do I have to annotate myself the transcripts with the gene go category + length?   > subset(supportedGenomes(), species == "Human" ...
goseq ensembl written 3.0 years ago by idomtamir10 • updated 3.0 years ago by Nadia Davidson270

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