Hi I recently upgraded to R 2.4.1 and ran biocLite to install the Bioconductor packages. This installs version 2.9.17 of limma. I also have my old version of R (2.1.1 which has version 2.3.3 of limma). When I run fit.O2<-lmFit(MA[isGene,], design.O2, weights=w) in R 2.4.1 I get the error message Error in asMatrixWeights(weights, dim(M)) : weights is of unexpected shape but this works fine in R 2.1.1 This is how I made my weights matrix: w<-modifyWeights(RG$weights,RG$genes$status,values=c("Cy3_oligo","Cy5_ oligo"), multipliers=0) excluded.spots<-spottypes[,1][spottypes[,1]!="cDNA"] w<-modifyWeights(RG$weights,RG$genes$status,values=excluded.spots, multipliers=0) # and then set anything with a weight of 0.1 to a value of 0 w[,][w[,]=="0.1"]<-0 the last four lines are using information from the spot types file. Can anyone tell me why this is happening? I really need the spot weights to be used. Thanks Nat Street --- Nathaniel Street ???????? University of Southampton ???????? Plants and Environment Lab ????? School of Biological Sciences ?? Basset Crescent East ?? Southampton ?SO16 7PX ?????? tel: +44 (0) 2380 594268 ? fax: +44 (0) 2380 594269 ?n.r.street at soton.ac.uk ??? http://www.populus.biol.soton.ac.uk/~nat http://del.icio.us/n.r.street

Dear Nat, > Date: Thu, 26 Apr 2007 10:15:00 +0100 > From: "Street N.R." <n.r.street at="" soton.ac.uk=""> > Subject: [BioC] weights in fitLM > To: <bioconductor at="" stat.math.ethz.ch=""> > > Hi > > I recently upgraded to R 2.4.1 and ran biocLite to install the Bioconductor packages. This > installs version 2.9.17 of limma. I also have my old version of R (2.1.1 which has version 2.3.3 > of limma). > > When I run > > fit.O2<-lmFit(MA[isGene,], design.O2, weights=w) > > in R 2.4.1 I get the error message > > Error in asMatrixWeights(weights, dim(M)) : > weights is of unexpected shape Well, the error message is already telling you what the problem is. You weights matrix is a different size to your data, which you can confirm by typing dim(w) dim(MA[isGene,]) It appears from the code you give that you've subsetted your data using isGene but haven't subsetted the weights matrix in the corresponding way. You probably need weights=w[isGene,]. This sort of error is something you should work towards trying to debug yourself. The error code suggests the problem, then you look closer at the arguments to see what the specific problem is. > but this works fine in R 2.1.1 Well, not fine, it just didn't give you an error message. It would appear that the more recent version has done you a favour by picking up your error. > This is how I made my weights matrix: > > w<-modifyWeights(RG$weights,RG$genes$status,values=c("Cy3_oligo","Cy 5_oligo"), multipliers=0) > > excluded.spots<-spottypes[,1][spottypes[,1]!="cDNA"] > w<-modifyWeights(RG$weights,RG$genes$status,values=excluded.spots, multipliers=0) > # and then set anything with a weight of 0.1 to a value of 0 > w[,][w[,]=="0.1"]<-0 This seems convoluted. Why set weights to 0.1 in the first place if you really want them to be zero? Best wishes Gordon > the last four lines are using information from the spot types file. > > Can anyone tell me why this is happening? I really need the spot weights to be used. > > Thanks > > Nat Street > --- > Nathaniel Street > ???????? University of Southampton > ???????? Plants and Environment Lab > ????? School of Biological Sciences > ?? Basset Crescent East > ?? Southampton > ?SO16 7PX > ?????? tel: +44 (0) 2380 594268 > ? fax: +44 (0) 2380 594269 > ?n.r.street at soton.ac.uk > > ??? http://www.populus.biol.soton.ac.uk/~nat > http://del.icio.us/n.r.street