Dear Gordon, I've tried out the new code on a larger, also problematic, dataset and it works without any problems. Many thanks, Cei On 7/27/12 4:31 AM, Gordon K Smyth wrote: > Hi Cei, > > This is now fixed in edgeR 2.99.3 on Bioc-devel. Your example now runs > with the results given below. Note that glmLRT now operates on the fit > object directly. The data object is no longer required as an argument. > > Best wishes > Gordon > > lrt <- glmLRT(fit, contrast=c(0,0,0,-1,0.5,0.5)) > topTags(lrt) > > Output: > Coefficient: -1*T2_S1 0.5*T2_S2 0.5*T2_S3 > logFC logCPM LR PValue FDR > CA00-XX-RX1-099-H06-EB.F 16.903 19.2 37.366 9.79e-10 1.08e-08 > Contig1405 2.446 18.0 10.440 1.23e-03 6.78e-03 > Cc_Contig7187 2.168 17.1 7.449 6.35e-03 2.33e-02 > Contig2423 -1.240 16.3 4.252 3.92e-02 1.08e-01 > CA00-XX-LP1-022-G05-EB.F -1.064 12.5 2.722 9.90e-02 2.18e-01 > Contig10618 0.699 13.1 0.913 3.39e-01 6.22e-01 > Cc_Contig2487 -0.506 15.8 0.658 4.17e-01 6.56e-01 > Contig6686 -0.387 12.6 0.337 5.62e-01 7.72e-01 > Contig15077 -0.279 15.8 0.198 6.56e-01 7.82e-01 > Contig7207 -0.247 12.2 0.137 7.11e-01 7.82e-01 > > > On Tue, 17 Jul 2012, Cei Abreu-Goodger wrote: > >> Hi guys, >> >> Many thanks for the update, I'll check the devel in a few weeks. >> >> Best, >> >> Cei >> >> On 7/16/12 11:35 PM, Gordon K Smyth wrote: >>> Dear Cei, >>> >>> Thanks for the nice reproducible example. >>> >>> We have been working on a programming solution to eliminate this >>> occasionally occuring error in edgeR. We have a nearly complete >>> solution in our local (non-public) version of edgeR. Running your data >>> example with our current local code, glmLRT no longer gives an error, >>> but the 9th row of your data generates a NA value for the likelihood >>> ratio test statistic. >>> >>> That's already an improvement, but I want to eliminate the NA fits as >>> well if possible. >>> >>> We will push this code out to Bioc-devel soon, but probably not before >>> the Bioconductor conference next week. >>> >>> Best wishes >>> Gordon >>> >>>> Date: Sun, 15 Jul 2012 18:36:16 -0500 >>>> From: Cei Abreu-Goodger <cei at="" langebio.cinvestav.mx=""> >>>> To: bioconductor at r-project.org >>>> Subject: [BioC] edgeR, glmLRT error >>>> >>>> Hi Gordon, >>>> >>>> I've been getting the following error upon running glmLRT: >>>> >>>> Error in beta[k, ] <- betaj[decr, ] >>>> NAs are not allowed in subscripted assignments >>>> >>>> which has previously been reported, for instance: >>>> >>>> https://stat.ethz.ch/pipermail/bioconductor/2011-February/038079.html >>>> >>>> I subsetted my count data (originally ~14k rows) to narrow down the >>>> culprit row, and I would like to send you this example in case it >>>> can be >>>> used to improve the glm fitting code. If it turns out to be impossible >>>> to completely avoid these kinds of errors, perhaps it would be nice to >>>> return the genes that are generating the NAs so that we can more easily >>>> remove them and proceed? >>>> >>>> I can also avoid this particular case by using only the CommonDisp or >>>> heavily increasing the prior.n, but that kind of defeats the purpose of >>>> the TagwiseDisp. >>>> >>>> Example code and sessionInfo: >>>> >>>> ################ >>>> library(edgeR) >>>> >>>> counts <- >>>> read.table("http://datos.langebio.cinvestav.mx/~cei/counts.tab") >>>> grp <- sub("_R.+", "", colnames(counts)) >>>> dge <- DGEList(counts=counts, group=grp) >>>> dge <- calcNormFactors(dge) >>>> >>>> design <- model.matrix(~0 + dge$samples$group) >>>> colnames(design) <- levels(dge$samples$group) >>>> >>>> dge <- estimateGLMCommonDisp(dge, design) >>>> dge <- estimateGLMTagwiseDisp(dge, design) >>>> >>>> fit <- glmFit(dge, design) >>>> lrt <- glmLRT(dge, fit, contrast=c(0,0,0,-1,0.5,0.5)) >>>> >>>> Error in beta[k, ] <- betaj[decr, ] : >>>> NAs are not allowed in subscripted assignments >>>> >>>> ################ >>>> R version 2.15.0 (2012-03-30) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] C/UTF-8/C/C/C/C >>>> >>>> attached base packages: >>>> [1] grDevices datasets stats graphics utils methods base >>>> >>>> other attached packages: >>>> [1] edgeR_2.6.9 limma_3.12.1 Biobase_2.16.0 >>>> BiocGenerics_0.2.0 BiocInstaller_1.4.7 >>>> >>>> ################ >>>> >>>> >>>> Many thanks, >>>> >>>> Cei >>>> >>>> -- >>>> Dr. Cei Abreu-Goodger >>>> Langebio CINVESTAV >>>> Tel: (52) 462 166 3006 >>>> cei at langebio.cinvestav.mx > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:18}}