hi Steve, Thanks for pointing me to this bug. I have fixed this in version 1.0.9. So now rlogTransformation should accept the given dds just like varianceStabilizingTransformation.
To avoid making a copy of the dds but still re-estimate dispersions, one can do: design(dds) <- ~ 1 mcols(dds)$dispersion <- NULL then either rlogTransformation or varianceStabilizingTransformation, which will call estimateDispersions internally. Mike On Sun, Apr 21, 2013 at 8:13 PM, Steve Lianoglou < mailinglist.honey...@gmail.com> wrote: > Hi Michael, > > On Sat, Apr 20, 2013 at 12:18 AM, Michael Love > <michaelisaiahl...@gmail.com> wrote: > > hi Steve, > > > > Thanks. Can you send a minimal example of the error? I can provide an > > alternate formula without error: > > > >> dds <- makeExampleDESeqDataSet() > >> design(dds) <- formula(~ condition) > >> rld <- rlogTransformation(dds) > > I'll see your `condition` and raise you a `treatment` :-) > > ======================= > R> set.seed(123) > R> library(DESeq2) > R> dds <- makeExampleDESeqDataSet() > R> colData(dds)$treatment <- factor(sample(c("x", "y"), ncol(dds), > replace=TRUE)) > R> design(dds) <- formula(~ condition + treatment) > > ## Fails for rlogTransformation > R> dds.rlog <- rlogTransformation(dds) > gene-wise dispersion estimates > mean-dispersion relationship > final dispersion estimates > Error in SummarizedExperiment(assays = rlogData(object, samplesVector, : > error in evaluating the argument 'assays' in selecting a method for > function 'SummarizedExperiment': Error in > modelMatrixNames[match(convertNames$from, modelMatrixNames)] <- > convertNames$to : > NAs are not allowed in subscripted assignments > > ## vst seems OK > R> dds.vst <- varianceStabilizingTransformation(dds) > gene-wise dispersion estimates > mean-dispersion relationship > final dispersion estimates > ======================== > > I'm using DESeq2_1.0.7 on R-3.0.0 > > Thanks, > -steve > > -- > Steve Lianoglou > Computational Biologist > Department of Bioinformatics and Computational Biology > Genentech > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel