Hi Hugo,

Thanks.

Could you possibly send me a small reproducible example (dds object which
throws this error)? I've worked on the dispersion estimation in the
development version, and this might clear up the error.

Mike
On Mar 11, 2014 10:55 AM, "Hugo Varet" <hugo.varet@pasteur.fr> wrote:

>  Sure, here it is :
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
> LC_MONETARY=French_France.1252 LC_NUMERIC=C
> [5] LC_TIME=French_France.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] DESeq2_1.2.10             RcppArmadillo_0.4.100.2.1
> Rcpp_0.11.0               GenomicRanges_1.14.4
> XVector_0.2.0
> [6] IRanges_1.20.7            BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
>  [1] annotate_1.40.1      AnnotationDbi_1.24.0 Biobase_2.22.0
> DBI_0.2-7            genefilter_1.44.0    grid_3.0.2
> lattice_0.20-27
>  [8] locfit_1.5-9.1       RColorBrewer_1.0-5   RSQLite_0.11.4
> splines_3.0.2        stats4_3.0.2         survival_2.37-7
> XML_3.98-1.1
> [15] xtable_1.7-3
>
> Hugo
>
> Hugo Varet
> Plate-Forme Transcriptome et Epigénome
> Institut Pasteur
> Mél. : hugo.varet@pasteur.fr
> Tél. : 01-40-61-35-13
>
> Le 11/03/2014 15:50, Michael Love a écrit :
>
> 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
>>
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>>
>
>

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