Hi Mike, thank you for having fixed the error so quickly ! I've just tried version 1.3.48, it works without any error on my data set. Best regards, Hugo Hugo Varet Plate-Forme Transcriptome et Epig?nome Institut Pasteur M?l. : hugo.varet at pasteur.fr T?l. : 01-40-61-35-13 Le 11/03/2014 23:02, Michael Love a ?crit : > hi Hugo, > > I've commited DESeq2 version 1.3.48, which fixes the error when I run your dds. > > Mike > > On Tue, Mar 11, 2014 at 1:02 PM, Michael Love > <michaelisaiahlove at="" gmail.com=""> wrote: >> Hi Hugo, >> >> Thanks for the reproducible example. This also occurs in devel. I'll >> email when I've come up with a fix. >> >> Meanwhile, i think the following line should resolve the error, which >> centers and scales the continuous variable. If you want the log2 fold >> change back on the original scale by afterwards dividing out >> attr(colData(dds)$conti, "scaled:scale"). >> >>> colData(dds)$conti <- scale(colData(dds)$conti) >>> DESeq(dds) >> using pre-existing size factors >> estimating dispersions >> gene-wise dispersion estimates >> mean-dispersion relationship >> final dispersion estimates >> fitting model and testing >> class: DESeqDataSet >> dim: 14499 16 >> exptData(0): >> assays(3): counts mu cooks >> rownames(14499): feature1 feature2 ... feature14498 feature14499 >> rowData metadata column names(29): baseMean baseVar ... deviance >> maxCooks >> colnames(16): sample1 sample2 ... sample15 sample16 >> colData names(4): sample dicho conti sizeFactor >> >> >> >> Mike >> >> On Tue, Mar 11, 2014 at 11:12 AM, Michael Love >> <michaelisaiahlove at="" gmail.com=""> wrote: >>> Hi Hugo, >>> >>> Thanks. >>> >>> Could you possibly send me a small reproducible example (dds object which >>> throws this error)? I've worked on the dispersion estimation in the >>> development version, and this might clear up the error. >>> >>> Mike >>> >>> On Mar 11, 2014 10:55 AM, "Hugo Varet" <hugo.varet at="" pasteur.fr=""> wrote: >>>> Sure, here it is : >>>> >>>> R version 3.0.2 (2013-09-25) >>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>> >>>> locale: >>>> [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 >>>> LC_MONETARY=French_France.1252 LC_NUMERIC=C >>>> [5] LC_TIME=French_France.1252 >>>> >>>> attached base packages: >>>> [1] parallel stats graphics grDevices utils datasets methods >>>> base >>>> >>>> other attached packages: >>>> [1] DESeq2_1.2.10 RcppArmadillo_0.4.100.2.1 Rcpp_0.11.0 >>>> GenomicRanges_1.14.4 XVector_0.2.0 >>>> [6] IRanges_1.20.7 BiocGenerics_0.8.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.40.1 AnnotationDbi_1.24.0 Biobase_2.22.0 >>>> DBI_0.2-7 genefilter_1.44.0 grid_3.0.2 >>>> lattice_0.20-27 >>>> [8] locfit_1.5-9.1 RColorBrewer_1.0-5 RSQLite_0.11.4 >>>> splines_3.0.2 stats4_3.0.2 survival_2.37-7 XML_3.98-1.1 >>>> [15] xtable_1.7-3 >>>> >>>> Hugo >>>> >>>> Hugo Varet >>>> Plate-Forme Transcriptome et Epig?nome >>>> Institut Pasteur >>>> M?l. : hugo.varet at pasteur.fr >>>> T?l. : 01-40-61-35-13 >>>> >>>> Le 11/03/2014 15:50, Michael Love a ?crit : >>>> >>>> Hi Hugo, >>>> >>>> Can you provide the ouput of sessionInfo() >>>> >>>> Mike >>>> >>>> On Mar 11, 2014 10:38 AM, "Hugo Varet" <hugo.varet at="" pasteur.fr=""> wrote: >>>>> Dear Mike Love and list members, >>>>> >>>>> I'm running DESeq2 with a design containing two covariates: the first is >>>>> dichotomous while the second is continuous. Here is the data.frame I put in >>>>> colData(dds): >>>>> sample dicho conti >>>>> 1 0 4.577032 >>>>> 2 0 4.462997 >>>>> 3 1 5.024896 >>>>> 4 1 4.543696 >>>>> 5 1 5.542576 >>>>> 6 1 5.356217 >>>>> 7 1 4.593729 >>>>> 8 1 4.243286 >>>>> 9 1 5.164055 >>>>> 10 0 4.565966 >>>>> 11 0 4.565966 >>>>> 12 0 4.760724 >>>>> 13 1 5.428459 >>>>> 14 1 4.515874 >>>>> 15 1 4.412964 >>>>> 16 1 4.426836 >>>>> >>>>> I chose to study the design (~ dicho + conti) and to test the effect of >>>>> the continuous covariate on the counts (about 15,000 features). I can >>>>> compute the size factors, but when estimating the dispersions, I get the >>>>> following error: >>>>>> dds <- estimateDispersions(dds) >>>>> gene-wise dispersion estimates >>>>> error: inv(): matrix appears to be singular >>>>> Erreur : inv(): matrix appears to be singular >>>>> >>>>> I think the error does not come from the design which is of full rank and >>>>> which works if I use a subset of the features. Moreover, with a design as (~ >>>>> dicho + conti + dicho:conti), I do not meet the error ! Do you have any idea >>>>> of the origin of the problem ? >>>>> >>>>> Best regards, >>>>> >>>>> Hugo >>>>> >>>>> -- >>>>> Hugo Varet >>>>> Plate-Forme Transcriptome et Epig?nome >>>>> Institut Pasteur >>>>> M?l. : hugo.varet at pasteur.fr >>>>> T?l. : 01-40-61-35-13 >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>