Hello Dear all I have a question about topTable in limma package. Can i specify parameters of interest in topTable, i.e. it gives me specific parameters such as adj.P-value and logFC, not ID and names columns because both of them are caused to disorder output file of topTable. I would like to process our data in excel limma(library) targets=readTargets("ApoAITargets.txt") RG=read.maimages(targets$FileName, source="spot") MA=normalizeWithinArrays(RG, method="loess") controlRef=rep(1,16) KOcontrol=c(rep(0,8),rep(1,8)) design=cbind(controlRef,KOcontrol) fit=lmFit(MA,design) fit=eBayes(fit) option(digits=3) result=topTable(fit, coef=2, number=6384, adjust="BH") as.matrix(result) write.csv(result,file="printtiploess.csv", quote=FALSE, col.names=TRUE, sep=",") Regards -- *S. Fazeli MSc Student of Chem. Eng. ferdowsi University mashhad Iran* [[alternative HTML version deleted]]

On Mon, Apr 25, 2011 at 11:53 PM, samane fazeli <samanefazeli at="" gmail.com=""> wrote: > ???Hello > ?Dear all > ?I have a question about topTable in limma package. Can i specify > parameters of interest in > ?topTable, i.e. it gives me specific parameters such as adj.P-value > and logFC, not ID and names > ?columns because both of them are caused to disorder output file of > topTable. I would like to > ?process our data in excel > > ?limma(library) > ?????targets=readTargets("ApoAITargets.txt") > ?RG=read.maimages(targets$FileName, source="spot") > ?MA=normalizeWithinArrays(RG, method="loess") > ?controlRef=rep(1,16) > ?KOcontrol=c(rep(0,8),rep(1,8)) > ?design=cbind(controlRef,KOcontrol) > ?fit=lmFit(MA,design) > ?fit=eBayes(fit) > ?option(digits=3) > ?result=topTable(fit, coef=2, number=6384, adjust="BH") > ?as.matrix(result) > ?write.csv(result,file="printtiploess.csv", quote=FALSE, col.names=TRUE, > ?sep=",") Hi. See the genelist argument to topTable(). Sean