James Wettenhall, kindly, sent me some explanations on how to accomplish the analyses without some genes. However, I tried to accomplish the procedure and I didn't get. I am sure that I didn't get because I don't have experience with the softwere R, because I believe that my doubt is related with the softwere R. Really, I don't know anything about R, I am learning how to work with R, with the packages of Bioconductor and with microarrays analyses now (and english too)! Everything this concomitant! I also know that it is very annoying (importunate) to be answering to basic questions, of beginners. But, to me it doesn't remain another option and I apologize with all you for proceeding of this sort things out. James wrote me that it was possible to accomplish a subset of the sample using one of the following resources: MAnocontrols < - MA[RG$genes [, "ID"] != "control",] or status < - rep ("gene",nrow(RG$genes)) status[grep ("control",RG$genes [, "ID"])] < - "control" MAnocontrols2 < - MA[status!= "control",] I tried to execute the analyses and I didn't get. Errors happened. At the end of this message I am enclosing the steps that I proceeded to accomplish the analysis. In my file of data for the analysis (Imagene ou put file) have some genes which I would not like that they were considered in the analysis. I would like to execute the normalizations without these genes, because the same ones are interfering negatively in them analysis. How could I accomplish these analyses? thanks a lot Marcelo +++++++++++++ > RegianeSample<-read.table("regianeRicoPobre.txt",header=TRUE,sep="\t", as.is= TRUE) > slides<-cbind(RegianeSample$FileNameCy3, RegianeSample$FileNameCy5) > RG<-read.maimages(slides, source="imagene") Read header information Read lamina1_1_selected.txt Read lamina1_0_selected.txt Read lamina2_1_selected.txt Read lamina2_0_selected.txt Read lamina3_1_selected.txt Read lamina3_0_selected.txt > layout<-RG$printer > genes<-RG$genes > MAsemplaca <- MA[RG$genes[,"Gene ID"]!="Sem Placa",] Error in "[.MAList"(MA, RG$genes[, "Gene ID"] != "Sem Placa", ) : (subscript) logical subscript too long > status <- rep("gene",nrow(RG$genes)) > status[grep("Sem Placa",RG$genes[,"Gene ID"])] <- "Sem Placa" Error in grep(pattern, x, ignore.case, extended, value, fixed) : invalid argument > MAraw <- MA.RG(RG) > MA <- normalizeWithinArrays(RG,layout) > MAsemplaca <- MA[RG$genes[,"Gene ID"]!="Sem Placa",] > design=c(1,-1,-1) > fit <- lm.series(MA$M,design) > eb <- ebayes(fit) > qqt(eb$t,df=fit$df+eb$df,pch=16,cex=0.1) > options(digits=3) > toptable(number=50, genelist=genes, fit=fit, eb=eb, adjust="fdr") Field Meta.Row Meta.Column Row Column Gene.ID 3769 XDM/BCYE 3 1 30 1 Sem Placa "Sem Placa" is the first gene in the top 50! -----Original Message----- From: James Wettenhall [mailto:wettenhall@wehi.edu.au] Sent: sexta-feira, 24 de outubro de 2003 02:46 To: Marcelo Luiz de Laia Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Remove some genes from analysis in limma package? Is it possible? Marcelo, RG and MA objects in limma are subsettable, so you can select the genes you want, e.g. MAnocontrols <- MA[RG$genes[,"ID"]!="control",] or you might want to define a "status" vector, as used in the plotMA function: status <- rep("gene",nrow(RG$genes)) status[grep("control",RG$genes[,"ID"])] <- "control" MAnocontrols2 <- MA[status!="control",] The "grep" method allows you to select multiple spots and give them the same spot type status, e.g. Calibration_Control_1 and Calibration_Control_2 could all be given the spot type "calibration" and then excluded from the analysis. You could replace "control" above by "ZZZZXXX21". Hope this helps, James ---------------------------------------------------------------------- ---- James Wettenhall Tel: (+61 3) 9345 2629 Division of Genetics and Bioinformatics Fax: (+61 3) 9347 0852 The Walter & Eliza Hall Institute E-mail: wettenhall@wehi.edu.au of Medical Research, Mobile: (+61 / 0 ) 438 527 921 1G Royal Parade, Parkville, Vic 3050, Australia http://www.wehi.edu.au ---------------------------------------------------------------------- ---- --- Incoming mail is certified Virus Free. ---