using RMA normalized microarray in Limma
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.
• 972 views
•
link
1 answer
Arrays do not have counts. RMA-proceased data are fine. See limma user guide.
• 0 views
•
link
Log in to answer this question.