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: [email protected] <mailto:[email protected]>
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