[Bioc-devel] baySeq countData class bug?

Message: 5
Date: Fri, 20 Feb 2015 11:55:21 +0200
From: Panagiotis Moulos<moulos at fleming.gr>
To:"bioc-devel at r-project.org"  <bioc-devel at r-project.org>
Subject: [Bioc-devel] baySeq countData class bug?
Message-ID:<54E70489.8050108 at fleming.gr>
Content-Type: text/plain; charset="UTF-8"

Hello,

In the previous Bioconductor release (2.14), a countData object from the
baySeq package could be accessed by sample names. Now it seems that it
can be accessed only by indices (version 2.0.50). Was this done on
purpose or is it a bug unnoticed so far? I discovered this as baySeq
fails with my package metaseqR. Some steps to reproduce:

library(metaseqR)
data("mm9.gene.data",package="metaseqR")
result <- metaseqr(
         counts=mm9.gene.counts,
         sample.list=sample.list.mm9,
         contrast=c("e14.5_vs_adult_8_weeks"),
         libsize.list=libsize.list.mm9,
         annotation="embedded",
         id.col=4,
         gc.col=5,
         name.col=7,
         bt.col=8,
         org="mm9",
         count.type="gene",
         normalization="edger",
         statistics="bayseq",
         qc.plots="mds",
         pcut=0.05,
         fig.format="png",
         export.what=c("annotation","p.value","fold.change"),
         export.scale="log2",
         export.values="normalized",
         export.stats="mean",
         export.where="~/bayseq_test",
         out.list=TRUE
)

crashes with: Error in r[i1] - r[-length(r):-(length(r) - lag + 1L)] :
non-numeric argument to binary operator

and the problem stems from the countData class:

object <- metaseqR::normalize.edger(mm9.gene.counts[,9:12],sample.list.mm9)
CD <- new("countData",data=object,replicates=c(
"e14.5","e14.5","adult_8_weeks","adult_8_weeks"))
baySeq::libsizes(CD) <- baySeq::getLibsizes(CD)

and then

cd <- CD[,c("e14.5_1","e14.5_2")]

crashes with

Error in r[i1] - r[-length(r):-(length(r) - lag + 1L)] :
    non-numeric argument to binary operator

while

cd <- CD[,1:2]

works. In the version released with Bioconductor 2.14, this was not
happening and the countData object could be accessed by sample names.
Thanks in advance for informing me whether this is a bug or if it will
remain like this from now on so I can update my code.

Panagiotis

-- *Panagiotis Moulos* Post doctoral researcher Biomedical Sciences 
Research Center 'Alexander Fleming' Fleming 34, 16672, Vari, Greece 
e-mail: moulos at fleming.gr <mailto:moulos at fleming.gr> [[alternative 
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