[BioC] DEXseq error on estimatelog2FoldChanges

[Alejandro Reyes]

Dear Fabrice Tourre,

Thanks for your answers.  If I understood correctly, you have only one 
control and one knockdown, without replication?  The errors are likely 
because of this (sorry if the messages are not informative enough!).

DEXSeq is designed to work with replicated data in order to distinguish 
biological variation from differences between your different biological 
conditions.  Unfortunately, if you have no replicates in your experiment 
you won't be able to estimate variation across replicates,  therefore 
not be able to test for differences in exon usage across biological 
conditions. There are many papers (e.g. doi:10.1186/gb-2010-11-10-r106, 
10.1038/nprot.2013.099, 10.1101/gr.133744.111) and discussions (e.g. in 
SeqAnswers) about why this is relevant.

Best regards,
Alejandro





> 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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