Dear R users,

I'am using marray and Limma packages to analyze genepix output.
1) how can I filter bad spots from my data (data contains 3 types of bad
spots).
my experiment contains 12 samples and the bad spot are not associated to the
same probes

2) how can I remove control probes from my data ?

I'm sorry, i'm new with R and I can't find answer in packages doc.

best regards,
Claire Pujoll
Paris, France

library(marray)
library(limma)
.......
Rawdata <- read.GenePix(targets=Macro_Mono_targets,skip=107)

design<- cbind(individual=c(0,0,1,1,2,2,3,3,4,4,5,5),
dim1=c(1,0,1,0,1,0,1,0,1,0,1,0),dim2=c(0,1,0,1,0,1,0,1,0,1,0,1))
fit   <- lmFit( normdata@maM, design)
contrast.matrix<-makeContrasts(dim1vsdim2=dim2-dim1, levels=design)
fit2 <- contrasts.fit(fit,contrast.matrix)
fiteb <- eBayes(fit2)
Toptable <- topTable(fiteb,number = 10600,genelist=maGeneTable(normdata),
sort.by="P",
resort.by= "M", adjust="BY")
write.table(Toptable,file="RNG_Best_10000genes.txt", row.names=FALSE,
col.names=TRUE, sep="\t")

best regards

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