User: pecot

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pecot0
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Posts by pecot

<prev • 6 results • page 1 of 1 • next >
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Comment: C: lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotyp
... I upgraded to Ubuntu 16 and ... it works!!!!!!!!! I can't tell why it works now, but it might be helpful for others. Michael, thanks a lot for your comments!   ...
written 1 day ago by pecot0
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Comment: C: lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotyp
... No worries, I found a way to make it work. I'll try it again when I upgrade to Ubuntu 16, never knows. ...
written 7 days ago by pecot0
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Comment: A: lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotyp
... Sorry, I didn't have the opportunity to work on it. Everything shut down here because of Irma. I worked on a machine with Ubuntu 14.4. I tried to reinstall all packages and R, but nothing changed. I have the feeling that it's related to GCC as it says when I install DESeq2 that openMP is not workin ...
written 7 days ago by pecot0
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Comment: A: lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotyp
... I haven't tried on another machine, but if it works on yours, it means that mine has a problem. I fully reinstalled R and remove all libraries, reinstalled DESeq2, still the same... I suspect something more vicious, maybe related to GCC compiler or C++ libraries. I'll have a look at it next week, he ...
written 13 days ago by pecot0
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Comment: C: lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotyp
... With just 'results', I get this:  system.time({ + res <- results(dds, contrast=c("condition","US.RbKO","US.Wt")) + })    user  system elapsed  10.996  43.532   6.956 I tried 'lfcShrink': system.time({ + res <- lfcShrink(dds, contrast=c("condition","US.RbKO","US.Wt"), res=res) + }) It's bee ...
written 14 days ago by pecot0
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lfcshrink and rlog take forever to compute with a DESeqDataSet with many genotypes and conditions
... Hi,   I'm using deseq2 for a RNAseq experiment with 2 genotypes and 5 conditions (2 replicates for each combination of genotype and condition). When I use the deseq command to perform a comparison, I get different results if all experiments are in the DESeqDataSet than when only the 2 compared exp ...
deseq2 rlog lfcshrink written 15 days ago by pecot0

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