[BioC] combining hgu133a and hgu133b

[Steve Lianoglou]

Mayte,

I was skimming through some bioc-packages to get some inspiration and
stumbled on this package:

http://www.bioconductor.org/packages/2.10/bioc/html/virtualArray.html

I've never used it, but it advertises itself to do exactly what you'd
like, so perhaps you'll find it useful.

-steve

On Fri, Apr 27, 2012 at 5:01 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> 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



-- 
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