[BioC] DEXseq error on estimatelog2FoldChanges

[Alejandro Reyes]

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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