Hi group,
I am trying to replicate a dataset GSE4824 from a paper.
There are actually 3 platforms in them. But right now I am concentrating
only on one platform GPL570.This contains 6 arrays.
I have written the code to perform Microarray Suite version 5.0 (MAS 5.0)
using Affymetrix default analysis settings and global scaling as
normalization method. The trimmed mean target intensity of each array was
arbitrarily set to 250.After which median normalization.


>source("http://bioconductor.org/biocLite.R")

> biocLite("affy")

> library(affy)

> mydata <- ReadAffy()

>eset.mas5 = mas5(mydata,sc=250,normalize=TRUE)

> write.exprs(eset.mas5,"GSE4824_GPL570.txt",sep='\t')

>eset=exprs(eset.mas5)

>median = apply(eset, 2, median)

>median1=median(median)
>exprs<-eset/median*median1
>write.table(exprs,"GSE4824_GPL570_Median.txt",sep='\t')

Please let me know if the my code performs corectly the above task,
especially if last few steps would perform median normalization correctly or
not? Also let me know if this is the right way to do median normalization.
Thanks,
Viritha

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