Jose -- An error like this appeared in another recent email, I think because of a version mismatch between R and Bioconductor packages. I suggest you 1) update packages following the directions at http://www.bioconductor.org/docs/install-howto.html and 2) report back to the list. If you do not have success, then please add the output of sessionInfo() Martin Gordon Smyth <smyth at="" wehi.edu.au=""> writes: > Dear Jose, > > The error message you give does not originate from any limma > function. In fact, I've never seen it before at all. > > The problem isn't likely to be with quality of your data in the > ordinary sense. It's more likely that the data are not want you think > in some way. > > To start finding the problem you might: > > 1. Use trace() to find in which function the error is occuring > > 2. Check you data, e.g. > > summary(subGeneIDMatrix[,c(2:3,16:17)]) > > If you write again, please give sessionInfo() etc. > > Best wishes > Gordon > >>Date: Mon, 29 Oct 2007 14:32:40 -0700 >>From: Jose Rodriguez <jarod07 at="" ucla.edu=""> >>Subject: [BioC] lmFit Error: "comparison of these types is not >> implemented" >>To: bioconductor at stat.math.ethz.ch >> >>I get the following error after executing the following command (using >>limma package for microarray analysis): >> >> > fit3< lmFit(subGeneIDMatrix[,c(2:3,16:17)],design) >>Error in fit3 < lmFit(subGeneIDMatrix[, c(2:3, 16:17)], design) : >> comparison of these types is not implemented >> >>The columns of the matrix I refer to are log transformed expression >>sets. The design matrix is simple: >> > design >> A B >>1 1 0 >>2 1 0 >>3 0 1 >>4 0 1 >>attr(,"assign") >>[1] 1 1 >>attr(,"contrasts") >>attr(,"contrasts")$`factor(c(1, 1, 2, 2))` >>[1] "contr.treatment" >> >>These two sets of data I am trying to compare are part of a larger >>experiment in which the error does not show up. Could the error be a bug >>or does it have something to do with the quality of this particular data >>subset? >>Thanks! > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor