[BioC] DEXseq error on estimatelog2FoldChanges

[Fabrice Tourre]

I am analyzing mouse samples.

> any( duplicated( paste( geneIDs(ecs), exonIDs(ecs), sep=":") ) )

[1] FALSE

> any( duplicated( featureNames(ecs)) )

[1] FALSE

> design(ecs)


                             countFile

~/projects/seqdata/data/tophat2/sample1/sample1.counts
~/projects/seqdata/data/tophat2/sample1/sample1.counts

~/projects/seqdata/data/tophat2/sample2/sample2.counts
~/projects/seqdata/data/tophat2/sample2/sample2.counts

                                                       condition    libType

~/projects/seqdata/data/tophat2/sample1/sample1.counts   control paired-end

~/projects/seqdata/data/tophat2/sample2/sample2.counts knockdown paired-end

On Tue, Feb 4, 2014 at 3:39 AM, Alejandro Reyes <alejandro.reyes at embl.de> wrote:
> Dear Fabrice Tourre,
>
> Thanks for your interest in DEXSeq and for the report!
> Some questions to get to the details of the warnings and
> the error message:
>
> 1. what is the output of doing:
>
> any( duplicated( paste( geneIDs(ecs), exonIDs(ecs), sep=":") ) )
> any( duplicated( featureNames(ecs)) )
>
> 2. What is the output of design(ecs) of your ExonCountSet object?
>
> Best regards,
> Alejandro
>
>
>
>> Dear expert,
>>
>> When I use DEXSeq to find different expressed exon, I got this error.
>> In my analysis, I only have two samples, one is case, one is control.
>>
>> ecs <- estimatelog2FoldChanges( ecs )
>> Error in `row.names<-.data.frame`(`*tmp*`, value = c("geneID", "exonID",
>> :
>>    duplicate 'row.names' are not allowed
>> In addition: There were 50 or more warnings (use warnings() to see the
>> first 50)
>>
>>
>> warnings()
>> Warning messages:
>> 1: In chol.default(XVX + lambda * I, pivot = TRUE) :
>>    the matrix is either rank-deficient or indefinite
>>
>>
>>
>> sessionInfo()
>> R version 3.0.0 (2013-04-03)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=C                 LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] DEXSeq_1.8.0       Biobase_2.22.0     BiocGenerics_0.8.0
>>
>> loaded via a namespace (and not attached):
>>   [1] biomaRt_2.18.0       Biostrings_2.30.1    bitops_1.0-6
>>   [4] GenomicRanges_1.14.4 hwriter_1.3          IRanges_1.20.6
>>   [7] RCurl_1.95-4.1       Rsamtools_1.14.2     statmod_1.4.18
>> [10] stats4_3.0.0         stringr_0.6.2        XML_3.98-1.1
>> [13] XVector_0.2.0        zlibbioc_1.8.0
>>
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>>
>