Just to copy the list, dropping empty levels fixed this bug:

ddsHTSeq$repSet <- droplevels(ddsHTSeq$repSet)

I will fix this in the devel branch.

Mike


On Wed, Jun 11, 2014 at 10:53 AM, Michael Love <michaelisaiahlove@gmail.com>
wrote:

> 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@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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>

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