Hi Hugo,

Can you provide the ouput of sessionInfo()

Mike
On Mar 11, 2014 10:38 AM, "Hugo Varet" <hugo.varet@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 Epigénome
> Institut Pasteur
> Mél. : hugo.varet@pasteur.fr
> Tél. : 01-40-61-35-13
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.
> science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

