[BioC] combining hgu133a and hgu133b

[James W. MacDonald]

Hi Mayte,

The short answer is no.

You could hypothetically create a mixture cdf that only contains 
probesets that are in the intersection of these three chip types and 
then normalize. Ben Bolstad has a page containing mixture cdfs for some 
arrays (http://bmbolstad.com/misc/mixtureCDF/MixtureCDF.html) but he 
never to my knowledge made one for the arrays you have.

In general, I think you would be better off to normalize separately and 
then combine.

Best,

Jim


On 4/27/2012 4:27 PM, Mayte Suarez-Farinas wrote:
> Hi all,
>
> I have HGU133a , HGU133b chips done in the same set of samples. Additionally I have hgu133plus2 chips in a different set of samples.
> Since "a+b" is almost "plus2", is tehre a way to combinethose  two affybatchs ?
>
> Any guidance will be appreciated!!
>
>
>
> Mayte Suarez-Farinas
> Research Assistant Professor,  Laboratory of Investigative Dermatology
> Biostatistician,  Center for Clinical and Translational Science
> The Rockefeller University
> 1230 York Ave, Box 178,
> New York, NY, 10065
> Phone: +1(212) 327-8213
> Fax:      +1(212) 327-8232
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099