Just for users who end up on this thread through search: updating to DESeq2 v1.4.5 clears up this hang. Mike On Sat, May 10, 2014 at 8:19 AM, Michael Love <michaelisaiahlove at="" gmail.com=""> wrote: > hi Carl, > > Thanks for reporting this. I had one user report such a hang for > version 1.2, and had implemented a fix for this in version 1.4, so I'm > not sure about this one. I could look into this if you could email me > off list a small example. Is it possible to find a small subset of > rows which produce the hang? > > ddssub <- dds[1:100,] > ddssub <- estimateDispersions(ddssub) > > And then to remove any identifying information, > > colData(ddssub) <- colData(ddssub)[, c("patient","proliferation") ] > levels(ddssub$patient) <- letters[ 1:nlevels(ddssub$patient) ] > > Mike > > On Fri, May 9, 2014 at 7:51 AM, Carl Herrmann > <c.herrmann at="" dkfz-heidelberg.de=""> wrote: >> Hi, >> >> I am analysing a patient dataset for diff. expression with DESeq2 (v >> 1.2.10). >> >> We have several patients, and for each patient we have several samples. >> I am running this analysis on different combinations of samples. >> >> My design has two factors : patient (multilevel) and a second factor >> (proliferation, true/false) >> so : design ~ patient + proliferation >> >> I am interested in diff. expression depending on the proliferation only >> (second factor). >> >> On some combinations, the gene dispersion estimation step >> (estimateDispersion) gets stuck at the gene-wise dispersion estimate. >> I let it run for several hours, and eventually killed the job. >> >> When reducing the number of iterations to 10, it gets stuck. Same problem >> with version DESeq2 v 1.4.0 >> >> Strangely, this happens when including samples that, when included in other >> combinations, run just fine. >> So this does not seem to be a problem of the dataset itself. >> >> I am not sure whether this is enough to get a hint on where the problem >> might come from, so please tell me whether I should provide additional >> information. >> >> Thanks for your help ! >> >> Carl >> >> -- >> ------------------------------------------------------------------ >> C a r l H E R R M A N N >> ------------------------------------------------------------------ >> Institut f?r Pharmazie und Molekulare Biotechnologie >> Universit?t Heidelberg >> DKFZ Heidelberg - Department of Theoretical Bioinformatics >> Im Neuenheimer Feld 580 >> D-69120 Heidelberg >> tel.: +49 (0) 6221 42-3612 >> email : c.herrmann at dkfz.de >> web: http://biologie.univ-mrs.fr/carlherrmann >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor