Dear Jay, Thanks for pointing out this error. Mea culpa -- I recently noticed that lmFit() wasn't setting Amean for the marrayNorm objects, and in fixing this have in fact broken lmFit() for marrayNorm objects. I've fixed this for limma 2.9.14. In the meantime, you can use library(convert) lm <- lmFit(as(snorm,"MAList"), design=c(1,-1,-1,1)) Best wishes Gordon At 10:00 PM 9/03/2007, bioconductor-request at stat.math.ethz.ch wrote: >Date: Thu, 8 Mar 2007 17:09:50 -0700 >From: Jay Konieczka <jayk at="" u.arizona.edu=""> >Subject: [BioC] marray and limma error with lmFit >To: bioconductor at stat.math.ethz.ch > >Hi, > >I'm getting an error for which I could not find help in the >archives. I recently reinstalled bioconductor (thinking, foolishly >perhaps, that I might be in need of an upgrade). Since doing so I >can't get lmFit to work for my data or even the swirl dataset. The >following produces the error given below the commands: > > > library(marray) >Loading required package: limma > > data(swirl) > > snorm = maNorm(swirl) > > lm = lmFit(snorm, design = c(1,-1,-1,1)) >Error in fit$Amean <- rowMeans(unwrapdups(object at maA, ndups = ndups, >spacing = spacing), : > object "fit" not found > > >I'm running R version 2.4.1 on Mac OS X 10.4.8 having installed >bioconductor via R using source("http://bioconductor.org/biocLite.R") >and biocLite() at the command line. > >Thanks, > >Jay > >-- >Jay H. Konieczka >Ph.D. Student, Antin Lab >Molecular & Cellular Biology >University of Arizona > >Phone: 1.520.591.3446 > >1656 E. Mabel, MRB 317 >Tucson, AZ 85724 USA >_____________________