[BioC] DESeq2 new error coming up

[Michael Love]

hi Marko,

Can you show what ddsHTSeq$repSet looks like?  Also what do you get
with table(ddsHTSeq$repSet)?


On Wed, Jun 11, 2014 at 8:19 AM, Marko Laakso <marko.laakso at significo.fi> wrote:
> Hi Michael,
>
>> The error is new because you are now using the v1.2 of DESeq2 which came
>> with the Bioconductor 2.13 release this month.  Maybe the system you are
>> working on automatically upgraded?
>>
>> The error you see is saying that you cannot subset the results DataFrame
>> with a vector that contains NAs. In the newest release of DESeq2 we have
>> included automatic independent filtering to optimize the number of genes
>> which will have FDR less than a given threshold.  The genes which are
>> filtered out get an adjusted p-value of NA  (this behavior can be turned
>> off by setting independentFiltering=FALSE to the results() function).
>
> I am getting the same error with the DESeqDataSet I have prepared directly
> from the HTSeq counts:
> ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
>                                        directory   = "/",
>                                        design      = ~ condition)
>
> The failing routine is called collapseReplicates:
> ddsHTSeq <- collapseReplicates(ddsHTSeq,
>                                groupby=ddsHTSeq$repSet, run=ddsHTSeq$repSet)
>
> Error in normalizeSingleBracketSubscript(i, x, byrow = TRUE, exact = FALSE) :
>   subscript contains NAs or out of bounds indices
>  Calls: main ... extractROWS -> extractROWS -> normalizeSingleBracketSubscript
>
> It seems that everything else is still working if I comment this
> collapseReplicates() call out. How can I fix ddsHTSeq so that
> collapseReplicates() would accept it or could you think of any other
> workarounds, which I could use to deal with my technical replicates?
>
> R version 3.1.0 (2014-04-10) -- "Spring Dance"
> Copyright (C) 2014 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
> Using Bioconductor version 2.14 (BiocInstaller 1.14.2)
>
> Package:           DESeq2
> Type:              Package
> Title:             Differential gene expression analysis based on the
>                    negative binomial distribution
> Version:           1.4.5
>
> Best regards,
> Marko
>
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