Entering edit mode
This isn't an error in limma of course, rather you have tried to use a
function (write.table) on an inappropriate object. Do you want to
output
the normalized log-ratios? If so, you might try
write.table(MA$M, file="your_file.txt",sep="\t")
Gordon
At 03:00 AM 1/12/2003, utepandragon@tiscali.it wrote:
>I use Limma Dev. Package and i'd like output my normalized data, but
i
>have a problem:
>
> > library(limma)
> > library(sma)
> >YourSample<-read.table("TargetsSampleTarget.txt",header=TRUE,sep="\
t",as.
> is=TRUE)
> > YourSample
> SlideNamber FileNameCy3 FileNameCy5 Cy3 Cy5
>1 1 slide1_1_Cy3.txt slide1_0_Cy5.txt Treated Untreated
>2 2 slide2_1_Cy3.txt slide2_0_Cy5.txt Treated Untreated
>3 3 slide3_1_Cy3.txt slide3_0_Cy5.txt Treated Untreated
> > slides<-cbind(YourSample$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
$ngrid
> .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]]
