Dear list, when using edgeR GLM after running estimateGLMCommonDisp I am getting this error: Error in solve.default(R, t(beta)) : system is computationally singular: reciprocal condition number = 1.11022e-16 It seems that there is not enough data for fitting the model (?), therefore I would like to ask you for your help. The design matrix for (~0 + groups + libraryType) looks like that(2 samples for each group). groups0h groups1h groups4h groups24h groups48h libraryTypesingle- end 1 1 0 0 0 0 0 2 1 0 0 0 0 0 3 0 1 0 0 0 0 4 0 1 0 0 0 0 5 0 0 1 0 0 0 6 0 0 1 0 0 0 7 0 0 0 1 0 0 8 0 0 0 1 0 0 9 0 0 0 0 1 1 10 0 0 0 0 1 1 Does anyone know how to overcome this problem? Thank you very much for your help. Tom -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_IE.UTF-8 LC_NUMERIC=C LC_TIME=en_IE.UTF-8 LC_COLLATE=en_IE.UTF-8 LC_MONETARY=en_IE.UTF-8 [6] LC_MESSAGES=en_IE.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.2 biomaRt_2.14.0 DESeq_1.10.1 [4] locfit_1.5-8 edgeR_3.0.0 limma_3.14.1 [7] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 GenomicFeatures_1.10.0 AnnotationDbi_1.20.1 [10] Biobase_2.18.0 ShortRead_1.16.0 latticeExtra_0.6-24 [13] RColorBrewer_1.0-5 Rsamtools_1.10.1 lattice_0.20-6 [16] Biostrings_2.26.2 GenomicRanges_1.10.2 IRanges_1.16.2 [19] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] annotate_1.36.0 bitops_1.0-4.1 BSgenome_1.26.1 DBI_0.2-5 genefilter_1.40.0 geneplotter_1.36.0 grid_2.15.1 [8] hwriter_1.3 RCurl_1.95-1.1 RSQLite_0.11.2 rtracklayer_1.18.0 splines_2.15.1 stats4_2.15.1 survival_2.36-14 [15] tools_2.15.1 XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

Hi Tom, On 10/15/2012 7:52 AM, Tom [guest] wrote: > Dear list, > > when using edgeR GLM after running estimateGLMCommonDisp I am getting this error: > > Error in solve.default(R, t(beta)) : > system is computationally singular: reciprocal condition number = 1.11022e-16 > > It seems that there is not enough data for fitting the model (?), therefore I would like to ask you for your help. > > > The design matrix for (~0 + groups + libraryType) looks like that(2 samples for each group). > > groups0h groups1h groups4h groups24h groups48h libraryTypesingle-end > 1 1 0 0 0 0 0 > 2 1 0 0 0 0 0 > 3 0 1 0 0 0 0 > 4 0 1 0 0 0 0 > 5 0 0 1 0 0 0 > 6 0 0 1 0 0 0 > 7 0 0 0 1 0 0 > 8 0 0 0 1 0 0 > 9 0 0 0 0 1 1 > 10 0 0 0 0 1 1 Your design matrix is not full rank, due to the fact that your 48hr samples are apparently also the only single-end library. What you are trying to do with this design matrix is to estimate the same coefficient twice (e.g., the coef for 48h is the same coef for single-end), which isn't possible. Offhand I can only think of three possibilities, all of which are suboptimal in some way. 1.) Ignore the fact that the 48h samples are single-end (e.g., remove the single-end column from your design matrix). 2.) Omit the 48h sample. 3.) Align all your data as single end, and then fit the model (without the single-end coef, obvs). All three suggestions have drawbacks, and only you can decide which one is the most palatable. There may be other possibilities, but none come readily to mind. Perhaps others will chime in. Best, Jim > > Does anyone know how to overcome this problem? > > Thank you very much for your help. > Tom > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_IE.UTF-8 LC_NUMERIC=C LC_TIME=en_IE.UTF-8 LC_COLLATE=en_IE.UTF-8 LC_MONETARY=en_IE.UTF-8 > [6] LC_MESSAGES=en_IE.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.8.2 biomaRt_2.14.0 DESeq_1.10.1 > [4] locfit_1.5-8 edgeR_3.0.0 limma_3.14.1 > [7] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 GenomicFeatures_1.10.0 AnnotationDbi_1.20.1 > [10] Biobase_2.18.0 ShortRead_1.16.0 latticeExtra_0.6-24 > [13] RColorBrewer_1.0-5 Rsamtools_1.10.1 lattice_0.20-6 > [16] Biostrings_2.26.2 GenomicRanges_1.10.2 IRanges_1.16.2 > [19] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] annotate_1.36.0 bitops_1.0-4.1 BSgenome_1.26.1 DBI_0.2-5 genefilter_1.40.0 geneplotter_1.36.0 grid_2.15.1 > [8] hwriter_1.3 RCurl_1.95-1.1 RSQLite_0.11.2 rtracklayer_1.18.0 splines_2.15.1 stats4_2.15.1 survival_2.36-14 > [15] tools_2.15.1 XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.4.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099