Meta-Analysis of Microarray data (Afyymetrix)

Question

[reza]

Hi everyone

I am doing a meta-analysis of microarray data (AffyMetrix; 4 sets). Normalization by RMA using the “Afyy” package in R and extraction of normalized data was done.

  >rawdata<-ReadAffy()

  >PM<-probes(rawdata,which="pm")

  >AffyInfo<-dimnames(PM)[[1]]

  >cutpos<-regexpr("\\d+$",AffyInfo,perl=T)

  >AffyID<-substr(AffyInfo,1,cutpos-1)

  >probe<-as.numeric(substr(AffyInfo,cutpos,nchar(AffyInfo)))

  >data.bgc<-bg.correct(rawdata,method="rma")

  >data.bgc.q<-normalize.AffyBatch.quantiles(data.bgc,type="pmonly")

   >pm.bgc.q<-probes(data.bgc.q,which="pm")

   >normalized<-cbind(AffyID,probe,pm.bgc.q)

   >write.table(normalized,file="NormalR.csv",sep=",",row.names=FALSE, quote=FALSE)

Now I want to know that normalization and extraction of normalized data have been done in the right way? If the answer is yes, how I can combine 4 .csv files (extracted from 4 sets) for downstream analysis to detect DEGs.

Thanks in advance