Hi
I am trying to combine data that was generated from different microarray platforms (MoGene_10_st and mouse4302)
when trying to filter genes using P/A calls, I ran into problems with MoGene since it does not have MM probes to run functions like mas5call 
instead I used Oligo package. The problem is when I run the function paCalls and then subset into normalized data I end up with control probes. To avoid that I am trying to remove control probes first then apply paCalls function, however, so far I could not find any function that allow me to do that with GeneFeatureSet which is initially generated through reading CEL files by oligo library
this is my code

library(oligo)
library(pd.mogene.1.0.st.v1)
geneCELs <- list.celfiles("C:\\Documents and Settings\\All Users\\Desktop\\Mouse data\\GSE37832_RAW\\MENSC", full.names = TRUE)
t<-read.celfiles(geneCELs)
probein<- getProbeInfo(t,  probeType = "pm", target = "probeset", sortBy = "none")
p<-paCalls(t, method="DABG")
indsum <- apply(p [,1:6], 1, function(x) sum(x[1:3] < 0.05) > 2 || sum(x[4:6] < 0.05) > 2)
pfinal <- p[insum,]
probesetids <- subset(probein, probein$fid %in% as.character(rownames(pfinal)))
dataset.1.mensc <-subset(mendsc.eset, rownames(mensc.eset) %in% as.character(probesetids$man_fsetid))  #mensc.est is normalized using expresso function
write.csv(dataset.1.mensc, "dataset.1.mensc.csv")
dim(dataset.1.mensc)


Shahenda

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