[BioC] combining hgu133a and hgu133b

[Steve Lianoglou]

Hi,

On Fri, Apr 27, 2012 at 4:51 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
> 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.

Wouldn't another approach be to use one of them there meta-analysis
type approaches, such as:

http://www.bioconductor.org/packages/2.10/bioc/html/RankProd.html or
http://www.bioconductor.org/packages/2.10/bioc/html/metaArray.html

or?

Never used them myself, but my mental note for these packages was
there for when I wanted to tackle such a situation (notes can be
wrong, of course -- mental ones, even more so since no ink was
actually invested).

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact