[BioC] edgeR: estimateGLMCommonDisp - Error in solve.default

[Tom [guest]]

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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