Meta-Analysis of Microarray data (Afyymetrix)
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23 months ago
reza ▴ 310

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.

Meta-Analysis Microarray Affymetrix R • 418 views