[BioC] DEXseq error on estimatelog2FoldChanges

[Fabrice Tourre]

Alejandro,

Thank you very much. Yes. I have only one control and one knockdown,
without replication. Do you have any suggestions how can I get the
differences in exon in two condition. Or different alternative
splicing in two different condition. DESeq2 can do this?

On Tue, Feb 4, 2014 at 9:18 AM, Alejandro Reyes <alejandro.reyes at embl.de> wrote:
> 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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>