Hi, I miss the Amean field in the output of eBayes() in limma 2.9.10 . It is there in limma 2.8.1 sample code: # Simulate gene expression data, # 6 microarrays and 100 genes with one gene differentially expressed set.seed(2004); invisible(runif(100)) M <- matrix(rnorm(100*6,sd=0.3),100,6) M[1,] <- M[1,] + 1 fit <- lmFit(M) # Ordinary t-statistic par(mfrow=c(1,2)) ordinary.t <- fit$coef / fit$stdev.unscaled / fit$sigma qqt(ordinary.t,df=fit$df.residual,main="Ordinary t") abline(0,1) # Moderated t-statistic eb <- eBayes(fit) # this returns FALSE with limma 2.9.10, TRUE with limma 2.8.1 "Amean" %in% names(eb) I run R 2.4.1. Do you experience the same? Thanks, Julien. -- Julien Gagneur EMBL/HTFG Center Tel: +49-(0)6221-387-8433 Fax: +49-(0)6221-387-8166 Email: julien.gagneur at embl.de Room 62 Meyerhofstrasse 1 D-69117 Heidelberg Germany

Q Nope, I just tried it (limma 2.9.10 under R2.4.1) and it's there. What has changed is topTable, from limma 2.9.3: "Changes to column headings from topTable: M is now logFC, A is now AveExpr" that threw me out at first as I didn't read the changeLog :-) Jose uoting Julien Gagneur <julien.gagneur at="" embl.de="">: > Hi, > > I miss the Amean field in the output of eBayes() in limma 2.9.10 . > > It is there in limma 2.8.1 > > sample code: > > # Simulate gene expression data, > # 6 microarrays and 100 genes with one gene differentially expressed > set.seed(2004); invisible(runif(100)) > M <- matrix(rnorm(100*6,sd=0.3),100,6) > M[1,] <- M[1,] + 1 > fit <- lmFit(M) > > # Ordinary t-statistic > par(mfrow=c(1,2)) > ordinary.t <- fit$coef / fit$stdev.unscaled / fit$sigma > qqt(ordinary.t,df=fit$df.residual,main="Ordinary t") > abline(0,1) > > # Moderated t-statistic > eb <- eBayes(fit) > > > # this returns FALSE with limma 2.9.10, TRUE with limma 2.8.1 > "Amean" %in% names(eb) > > > > I run R 2.4.1. Do you experience the same? > > Thanks, > Julien. > > -- > Julien Gagneur > EMBL/HTFG Center > Tel: +49-(0)6221-387-8433 > Fax: +49-(0)6221-387-8166 > Email: julien.gagneur at embl.de > > Room 62 > Meyerhofstrasse 1 > D-69117 Heidelberg > Germany > > _______________________________________________ > 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 > > -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK