Beginner's question: ebayes
2
0
Entering edit mode
@eliana-lucchinetti-zaugg-676
Last seen 10.2 years ago
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]]
limma limma • 979 views
ADD COMMENT
0
Entering edit mode
@vincent-j-carey-jr-4
Last seen 7 weeks ago
United States
> 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...
ADD COMMENT
0
Entering edit mode
@adaikalavan-ramasamy-675
Last seen 10.2 years ago
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 >
ADD COMMENT

Login before adding your answer.

Traffic: 290 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6