[BioC] Imitating Affy's own steps

[James W. MacDonald]

Timothy Wu wrote:
> On Mon, Apr 5, 2010 at 10:24 PM, James W. MacDonald
> <jmacdon at med.umich.edu>wrote:
> 
>> 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
>>
>>
> Thanks for the reply. It looks pretty close.
> 
> So is the expresso() command listed on the page
> *
> eset <- expresso(Data,
> bgcorrect.method="mas",normalize=FALSE,pmcorrect.method="mas",summary.method="mas")
> *
> 
> be the same as the justMAS()?

Well, the intent is the same, but the implementation is different, so I 
wouldn't be surprised if there were differences there as well.

Best,

Jim


> 
> Thanks in advance.
> 
> Timothy
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues