I use Limma Dev. Package and i'd like output my normalized data, but i have a problem: > library(limma) > library(sma) >YourSample<-read.table("TargetsSampleTarget.txt",header=TRUE,sep="\t" ,as.is=TRUE) > YourSample SlideNamber FileNameCy3 FileNameCy5 Cy3 Cy5 1 1 slide1_1_Cy3.txt slide1_0_Cy5.txt Treated Untreated 2 2 slide2_1_Cy3.txt slide2_0_Cy5.txt Treated Untreated 3 3 slide3_1_Cy3.txt slide3_0_Cy5.txt Treated Untreated > slides<-cbind(YourSample$FileNameCy3, YourSample$FileNameCy5) > RG<-read.maimages(slides, source="imagene") > RG<-read.maimages(slides, source="imagene") Read header information Read slide1_1_Cy3.txt Read slide1_0_Cy5.txt Read slide2_1_Cy3.txt Read slide2_0_Cy5.txt Read slide3_1_Cy3.txt Read slide3_0_Cy5.txt > layout<-RG$printer > genes<-RG$genes > plot.print.tip.lowess(RG,layout,pch=16,cex=0.1,image=3) > plot.print.tip.lowess(RG,layout,pch=16,cex=0.1,image=3,norm="p") > MAraw <- MA.RG(RG) >plot.scale.box(MAraw$M[,3],layout,col=rainbow(layout$ngrid.r*layout$n grid.c)) > abline(0,0) > MA <- normalizeWithinArrays(RG,layout) > write.table(MA, file="your_file.txt",sep="\t") Error in as.data.frame.default(x[[i]], optional = TRUE) : can't coerce MAList into a data.frame Can you help me? Thanks [[alternative HTML version deleted]]