[BioC] edgeR: estimateGLMCommonDisp - Error in solve.default
Tom [guest]
guest at bioconductor.org
Mon Oct 15 13:52:43 CEST 2012
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
--
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