Hi Steve, Thanks for pointing out this bug in the renaming code. I will fix this as soon as possible.
Best, Mike On Jul 10, 2013 1:00 AM, "Steve Lianoglou" <[email protected]> wrote: > Greetings DESeq2ers, > > I've been playing around with different ways to encode a 2x2 factorial > design I'm working with: 4 cell types, 4 treatments and exploring > what's cooking in there. > > I thought that the nested interaction formula used in the limma user's > guide (section 8.5.3) would be an easy way to explore some obvious > questions since differential expression from different treatments > within each cell type (among other things) shake out quite cleanly > from the results of running the wald test since these end up as > columns in the design matrix, eg: > > ~ cell + cell:treatment > > as long as the control treatment is the first level of the treatment > factor, we got columns for all cell:treatment effects, eg. > cellA:treatment1, cellA:treatment2, ..., cellD:treatment4) > > Yay! > > ... almost ... > > The problem is that the "renaming column" stuff in the fitNbinomGLMs > function seems to assume that we'll have columns for all main effects > in the design matrix, so the following line triggers an error: > > modelMatrixNames[match(convertNames$from, modelMatrixNames)] <- > convertNames$to > > since you will find elements like "treatment2, ..., treatment4" among > the elements in `covertNames$from`. The call to match then returns NA > for these, and *boom*. > > An easy fix would be to add the following line after the call to > `renameModelMatrixColumns`: > > convertNames <- subset(convertNames, from %in% modelMatrixNames) > > So the "if (renameCols)" block (line 1066 in core.R) now becomes: > > if (renameCols) { > names(modelMatrixNames) <- modelMatrixNames > convertNames <- renameModelMatrixColumns(modelMatrixNames, > > as.data.frame(colData(object)), > modelFormula) > convertNames <- subset(convertNames, from %in% modelMatrixNames) > modelMatrixNames[match(convertNames$from, modelMatrixNames)] <- > convertNames$to > } > > > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
