Meta-Analysis of Microarray data (Afyymetrix)
0
0
Entering edit mode
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.

Thanks in advance

Meta-Analysis Microarray Affymetrix R • 418 views
ADD COMMENT

Login before adding your answer.

Traffic: 1425 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6