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: mou...@fleming.gr <mailto:mou...@fleming.gr> [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel