[BioC] Imitating Affy's own steps

[James W. MacDonald]

Hi Timothy,

AFAIK, you have two choices. Using the affy package, you can use mas5() 
and mas5calls(). You can also use justMAS() from the simpleaffy package.

I don't believe either one will give you exactly the same results. For 
the affy package see

http://bmbolstad.com/misc/MAS5diff/Mas5difference.html

for an explanation of the differences.

Best,

Jim



Timothy Wu wrote:
> Hi,
> 
> If I want to replicate as close as possible (or exactly, is it possible?)
> the steps of Affy's software using Bioconductor packages, from background
> subtraction, normalization, summarization to finding differential gene
> expression. What's the best way to go about doing that? I've never used
> Affy's own software (I'm learning microarray processing through documents
> for bioconductor itself), but I want to make sure I'm doing things right by
> taking raw data from GEO and compare to author's own published result using
> Affy's standard methods before I switch to GCRMA, quantile, and median
> polish.
> 
> For data preprocessing, I notice that in Affy's package there are these
> options:
> mas for background methods
> mas5 for normalization
> mas for PM correct method
> mas for summarization methods
> 
> So are these the steps I should take?
> 
> How about for differential gene comparison? Which package should I use? Any
> pointer would be appreciated, thanks. :)
> 
> Timothy
> 
> 	[[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.
Ann Arbor MI 48109-5618
734-615-7826
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