[BioC] DESeq2 new error coming up

[Marko Laakso]

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