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

[Michael Love]

Hi Hugo,

Thanks for the reproducible example. This also occurs in devel. I'll
email when I've come up with a fix.

Meanwhile, i think the following line should resolve the error, which
centers and scales the continuous variable. If you want the log2 fold
change back on the original scale by afterwards dividing out
attr(colData(dds)$conti, "scaled:scale").

> colData(dds)$conti <- scale(colData(dds)$conti)
> DESeq(dds)
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
class: DESeqDataSet
dim: 14499 16
exptData(0):
assays(3): counts mu cooks
rownames(14499): feature1 feature2 ... feature14498 feature14499
rowData metadata column names(29): baseMean baseVar ... deviance
  maxCooks
colnames(16): sample1 sample2 ... sample15 sample16
colData names(4): sample dicho conti sizeFactor



Mike

On Tue, Mar 11, 2014 at 11:12 AM, Michael Love
<michaelisaiahlove at gmail.com> wrote:
> 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 at 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 at 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 at 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 at pasteur.fr
>>> Tél. : 01-40-61-35-13
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>