Dear Birger, Don't forget to state your limma version when you ask a question. Almost certainly you have a slightly out of data version. Reinstall limma and the example should work again, although with changed column names for topTable. Best wishes Gordon > Date: Thu, 19 Apr 2007 15:11:39 +0200 > From: "Hauchecorne Birger" <birger.hauchecorne at="" student.ua.ac.be=""> > Subject: [BioC] marray and limma error with lmFit > To: <bioconductor at="" stat.math.ethz.ch=""> > Cc: birgerhauchecorne at hotmail.com > Message-ID: > <a4e682b8a936374a9190a3a0fee412f22d18db at="" xmail10.ad.ua.ac.be=""> > Content-Type: text/plain > > Hi, > > I've got a little problem with lmFit and I was hoping you could help me. > > I'm following a book in order to analyse microarray data. The book I follow is "Bioinformatics and > Computational Biology Solutions Using R and Bioconductor" by Gentleman et al.. More precise > chapter 4 "Preprocessing Two-Color Spotted Arrays" by Yang and Paquet. > In order to get used to the protocol, I followed the example used in the book. > These are the procedures used: >>library(beta7) >>library(arrayQuality) >>Targetinfo<-read.marrayInfo("TargetBeta7.txt") >>mraw<-read.GenePix(targets=Targetinfo) >>normdata<-maNorm(mraw) >>library(convert) >>mdata<-as(normdata,"exprSet") > > And then in the book, they used this: >>LMres<-lmFit(normdata,design=c(1,-1,-1,1,1,-1),weights=NULL) > Error in fit$Amean <- rowMeans(unwrapdups(object at maA, ndups = ndups, spacing = spacing), : > object "fit" not found > > giving me an error. > > I searched for this in the net, and found a solution from you >>LMres<-lmFit(as(normdata,"MAList"),design=c(1,-1,-1,1,1,-1),weights= NULL) > > So I could continue with >>LMres<-eBayes(LMres) >>restable<-topTable(LMres,number=10,resort.by="M") > Error in order(na.last, decreasing, ...) : > argument 1 is not a vector > > giving me another error. I can't sort by M (a parameter I need) > By sorting on another parameter ("T" for example), I could generate a list nonetheless. In the > book there was a solution for the analysis, so I checked it with the list I found. Oddly enough > the values found for "M" in the book where equal to my "logFC" values, unfortunately I couldn't > sort on "logFC". > > Another odd thing that I found was the the resulting P.Value from the book (which was 1 for the > significant cases), was different from my P.Values (although the genes are the same). Most of the > time where it was supposed to be 1, I became 0. Unfortunately again, not all the time, so it was > impossible to tell where it was correct. > > I'm now thinking that the cause of this problem can be found in the solution you guys gave for the > first problem (>LMres<-lmFit(as(normdata,"MAList"),design=c(1,-1,-1, 1,1,-1),weights=NULL)) > > I was hoping you could help me with my problem why these P.values are different, and where is my > "M" column? > > > I'm using R 2.4.1. on windows XP having installed bioconductor. > > Kind regards and thanks in advance, > > Birger Hauchecorne > Senior Student Bio-Engineering at University of Antwerp, Belgium