Entering edit mode
Marko Laakso
▴
10
@marko-laakso-6601
Last seen 9.7 years ago
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
