[Bioc-devel] baySeq countData class bug?

[Panagiotis Moulos]

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>

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