using RMA normalized microarray in Limma
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Entering edit mode
12 weeks ago
Fluke ▴ 10

Hi, i downloaded raw.tar file containing .CEL microarray data from GEO database. and then i use affy() package in R to extracted .CEL file and normalized with RMA(). Can i use this expression data to put in Limma? or it is better to use raw count anf how can i get it? Here is my code.

setwd("/Users/Admin LMB/OneDrive/Document/CEL FILE")
getwd() 
list.files()
library(affy)
Data<-ReadAffy() 
sampleNames(Data) 
N=length(Data)
eset.rma<-rma(Data)
exprs<-exprs(eset.rma)
probeid<-rownames(exprs)
exprs<-cbind(probeid,exprs) 
write.table(exprs,file="expression.txt",sep='\t',quote=F,row.names=F)

Thanks in advanced.

GEOdatabase Microarray limma RMA • 284 views
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Entering edit mode
12 weeks ago
ATpoint 80k

Arrays do not have counts. RMA-proceased data are fine. See limma user guide.

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