[BioC] median normalization

[James W. MacDonald]

Hi Viritha,

On 8/29/2011 12:10 PM, viritha kaza wrote:
> 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

The output from mas5() isn't log transformed, so you should be 
subtracting and adding, not dividing and multiplying.

This assumes that by 'median normalization' the original authors simply 
meant median centering.

Best,

Jim


>> 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
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
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734-615-7826
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