Hi there, I'm trying to subset an Marraylist in limma to remove low intensity values before fitting the linear model. Forgive me if I'm missing something obvious, I'm a novice at R. Here's what I'm doing: A.filter<-MA$A<10 MA.filterd<-MA[A.filter,] But I get: Error in '[.MAList'(MA,A.filter, ) : (subscript) logical subscript too long It seems to be similar to what's shown in the user guide under the Weaver data: isGene <- MA$genes$Status == "Riken" fit <- lmFit(MA[isGene, ], design) Any help is appreciated D

D <spam56 at="" gto.net=""> writes: > Hi there, > > I'm trying to subset an Marraylist in limma to remove low intensity > values before fitting the linear model. Forgive me if I'm missing > something obvious, I'm a novice at R. Here's what I'm doing: > > A.filter<-MA$A<10 > MA.filterd<-MA[A.filter,] > > But I get: > > Error in '[.MAList'(MA,A.filter, ) : (subscript) logical subscript too long I notice that MA.filterd has a 'd' on the end of it, and bet that dim(MA.filtered) has fewer rows than length(MA.A.filter). Martin > It seems to be similar to what's shown in the user guide under the Weaver data: > > isGene <- MA$genes$Status == "Riken" > fit <- lmFit(MA[isGene, ], design) > > Any help is appreciated > > D > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org

Dear D, as a general remark that may also be relevant to some others here, I think you would have a better chance of getting replies to your posts if you revealed your real name. I for one rarely feel inclined to answer to anonymous posts. You may also want to read the posting guide, there are a number of helpful suggestions that may help you to have more meaningful interactions: http://www.bioconductor.org/docs/postingGuide.html Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber ha scritto: > Hi there, > > I'm trying to subset an Marraylist in limma to remove low intensity values > before fitting the linear model. Forgive me if I'm missing something obvious, > I'm a novice at R. Here's what I'm doing: > > A.filter<-MA$A<10 > MA.filterd<-MA[A.filter,] > > But I get: > > Error in '[.MAList'(MA,A.filter, ) : (subscript) logical subscript too long > > It seems to be similar to what's shown in the user guide under the Weaver data: > > isGene <- MA$genes$Status == "Riken" > fit <- lmFit(MA[isGene, ], design) > > Any help is appreciated > > D >