[BioC] Limma coerce error

[Gordon Smyth]

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 at 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
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