Hi Alexander, Thanks for your rapid response! DEXSeq is designed to test for differences in exon usage, not differential > expression. I guess I should clarify--I have already used edgeR to look for overall differential expression but was also wanting to see if I could pin down functional components where the DE is occurring, i.e. which exon(s). Anyway, in both DESeq and DEXSeq you can assign normalization factors using: > > sizeFactors(yourobject) <- your normalization factors > > or why dont you use the normalization factors from DESeq/DEXSeq? Thanks a bunch! I should have read the sizeFactors documentation more carefully. The reason I really wanted to be able to supply my own normalization factors is because we have some large sample-specific GC effects on expression that most normalization techniques will be unable to take into account. Using conditional quantile normalization (cqn from bioconductor) has shown a large improvement in our count distributions. Also, there are no issues with a single core. I was just hoping to parallelize the process since it takes several hours with our dataset to run. Thanks again, Alicia On Tue, Oct 9, 2012 at 1:37 AM, Alejandro Reyes <alejandro.reyes@embl.de>wrote: > Dear Alicia, > > Thanks for your input! > > > Hi all, >> >> I am interested in using DEXSeq to look for differential expression >> across seven conditions, each with ~7 biological replicates. I have created >> an ExonCountSet object and am trying to estimate the dispersions from my >> model. I have two questions: 1) Is it possible to supply an offset term to >> the glm? This would be very helpful when trying to incorporate >> normalization info, since the count data is restricted to integers. I >> noticed that the glmnb.fit object called by DEXSeq contains a mf$offset >> variable. Additionally, 2) Has anyone seen and/or corrected the following >> error when trying to use multiple cores to estimate dispersions? >> > > DEXSeq is designed to test for differences in exon usage, not differential > expression. To test for differential expression you can use other packages > like DESeq or edgeR. Anyway, in both DESeq and DEXSeq you can assign > normalization factors using: > > sizeFactors(yourobject) <- your normalization factors > > or why dont you use the normalization factors from DESeq/DEXSeq? > > > ecs <- estimateDispersions(ecs, nCores=3) >> Estimating Cox-Reid exon dispersion estimates using 3 cores. (Progress >> report: one dot per 100 genes) >> The process has forked and you cannot use this CoreFoundation >> functionality safely. You MUST exec(). >> Break on __THE_PROCESS_HAS_FORKED_AND_**YOU_CANNOT_USE_THIS_** >> COREFOUNDATION_FUNCTIONALITY__**_YOU_MUST_EXEC__() to debug. >> This message repeats several times and also contains the following: >> Tcl_ServiceModeHook: Notifier not initialized. >> > > If you are testing for differential exon usage, do you get the error > message using only a single core? I believe that it is a problem with your > multicore + apple... some "googling" took me to this: > > https://stat.ethz.ch/**pipermail/r-sig- mac/2009-**August/006426.html<https: stat.ethz.ch="" pipermail="" r-sig-="" mac="" 2009-august="" 006426.html=""> > > Best wishes, > Alejandro > > > Thanks a bunch for any potential insight! >> >> -- output of sessionInfo(): >> >> sessionInfo() >>> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-apple-darwin12.0.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.**UTF-8/C/en_US.UTF-8/en_US.UTF-**8 >> >> attached base packages: >> [1] splines stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] DEXSeq_1.2.1 Biobase_2.16.0 BiocGenerics_0.2.0 >> [4] RColorBrewer_1.0-5 scales_0.2.2 cqn_1.2.0 >> [7] quantreg_4.91 SparseM_0.96 preprocessCore_1.18.0 >> [10] nor1mix_1.1-3 mclust_4.0 plyr_1.7.1 >> [13] multicore_0.1-7 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.12.0 colorspace_1.1-1 dichromat_1.2-4 hwriter_1.3 >> [5] labeling_0.1 munsell_0.4 RCurl_1.95-0 statmod_1.4.16 >> [9] stringr_0.6.1 tcltk_2.15.1 tools_2.15.1 XML_3.95-0 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> > [[alternative HTML version deleted]]