Gee, thanks Jim. I was worrying my "Documentation"-interpretation abilities had suffered from the good weather period the last days here in hamburg. :-) Regards, Benjamin -----Urspr?ngliche Nachricht----- Von: James W. MacDonald [mailto:jmacdon at med.umich.edu] Gesendet: 25 October 2006 17:10 An: Benjamin Otto Cc: BioClist Betreff: Re: [BioC] lmFit(eset,design) error message Hi Benjamin, I don't think you are doing anything wrong (other than calling an ExpressionSet an exprSet ;-D). The problem here is that lmFit() hasn't been updated to accept an ExpressionSet object, so it is erroring out. As you note, lmFit() will accept a matrix, so if you extract the expression values into a matrix using the exprs() accessor, it will work. For now I think that is the best work-around. Best, Jim Benjamin Otto wrote: > Hi, > > > > Although I can't imagine I'm the first one to get the error message > unfortunately my gmane-searches were unsuccessful. When I apply limmas > lmFit() to an exprSet object I get the error message: > > > > "Error in as.vector(x, mode) : cannot coerce to vector" > > > > There is no problem using lmFit() with the expressionset table exprs(eset)! > According to the documentation it should be possible to directly use the > exprSet object. Here is an example code resulting in the error message with > me: > > > > >>library("ALL") > > >>library(limma) > > >>data("ALL") > > >>eset <- ALL[, ALL$mol.biol %in% c("BCR/ABL", "ALL1/AF4")] > > >>f <- factor(as.character(eset$mol.biol)) > > >>design <- model.matrix(~f) > > >>fit <- eBayes(lmFit(eset,design)) > > > > > --> Error in as.vector(x, mode) : cannot coerce to vector > > > > As already mentioned the following command works ok: > > > > >>fit <- eBayes(lmFit(exprs(eset),design)) > > > > > > > Has anyone observed the error before and if it is none then what am I doing > wrong? > > > > regards, > > > > Benjamin > > > > > > Version numbers: > > ---------------- > > R: 2.4.0 under WinXP > > Limma: 2.9.1 > > Biobase: 1.12.2 > > Tools: 2.4.0 > > ALL: 1.4.1 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.