Dear all: I've got 30 chips, 5 controls and 5 chips x5 treatment groups and decided that LIMMA would be the best to analyze these data. I am using this package for the first time (downloaded and installed today, March 16 2004) and I am thus following the manual instructions. But Alas! I've got the following error message: fit2 < eBayes(fit2) coefficients stdev.unscaled sigma df.residual method design contrasts TRUE TRUE FALSE TRUE FALSE TRUE FALSE df.prior s2.prior var.prior proportion s2.post t p.value FALSE FALSE FALSE FALSE TRUE TRUE FALSE lods FALSE Warning message: longer object length is not a multiple of shorter object length in: fit2 < eBayes(fit2). Because of this error, no information is extractable afterwards and obviously I get further error messages: topTable(fit2,coef=1, adjust="fdr") Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x), : attempt to set an attribute on NULL > clas <-classifyTests(fit2) Error in classifyTests(fit2) : tstat cannot be extracted from object Any idea of what went wrong? Thank you very much for any suggestions! ELIANA =============================== Eliana Lucchinetti Zaugg, PhD Institute of Pharmacology and Toxicology Section of Cardiovascular Research-Room 17 J 28 University of Zurich Winterthurerstr. 190 CH-8057 Zürich (Switzerland) Phone: +41-1-635 59 18 Fax: +41-1-635 68 71 e-mail: eliana.zaugg@pharma.unizh.ch [[alternative HTML version deleted]]

> Dear all: > I've got 30 chips, 5 controls and 5 chips x5 treatment groups and decided that LIMMA would be the best to analyze these data. > I am using this package for the first time (downloaded and installed today, March 16 2004) and I am thus following the manual instructions. But Alas! > I've got the following error message: > > fit2 < eBayes(fit2) note that you are using "<", a comparison operator, where i believe you intend "<-", an assignment operator. try fit2 <- eBayes(fit2) # unless you'd like to keep fit2 around...

fit2 <- eBayes(fit2) ^^^ > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Eliana > Lucchinetti Zaugg > Sent: 16 March 2004 10:26 > To: Bioconductor Mailing List > Subject: [BioC] Beginner's question: ebayes > Importance: High > > > Dear all: > I've got 30 chips, 5 controls and 5 chips x5 treatment groups and > decided that LIMMA would be the best to analyze these data. > I am using this package for the first time (downloaded and > installed today, March 16 2004) and I am thus following the > manual instructions. But Alas! > I've got the following error message: > > fit2 < eBayes(fit2) > coefficients stdev.unscaled sigma df.residual > method design contrasts > TRUE TRUE FALSE TRUE > FALSE TRUE FALSE > df.prior s2.prior var.prior proportion > s2.post t p.value > FALSE FALSE FALSE FALSE > TRUE TRUE FALSE > lods > FALSE > Warning message: > longer object length is not a multiple of shorter object length > in: fit2 < eBayes(fit2). > > Because of this error, no information is extractable afterwards > and obviously I get further error messages: > topTable(fit2,coef=1, adjust="fdr") > Error in array(x, c(length(x), 1), if (!is.null(names(x))) > list(names(x), : > attempt to set an attribute on NULL > > clas <-classifyTests(fit2) > Error in classifyTests(fit2) : tstat cannot be extracted from object > > Any idea of what went wrong? > Thank you very much for any suggestions! > ELIANA > > =============================== > Eliana Lucchinetti Zaugg, PhD > Institute of Pharmacology and Toxicology > Section of Cardiovascular Research-Room 17 J 28 > University of Zurich > Winterthurerstr. 190 > CH-8057 Z?rich (Switzerland) > > Phone: +41-1-635 59 18 > Fax: +41-1-635 68 71 > e-mail: eliana.zaugg@pharma.unizh.ch > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >