[BioC] DESeq2 error: inv(): matrix appears to be singular

[Hugo Varet]

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 Epigénome
Institut Pasteur
Mél. : hugo.varet at pasteur.fr
Tél. : 01-40-61-35-13