[BioC] questions about RLMM

[Rafael A. Irizarry]

Yen-Tsung,

As Jim points out the oligo package can handle this data. The 
"crlmm" function will implement a calling algorithm we have just finished 
fine-tunning. You can read about it here:

http://www.bepress.com/jhubiostat/paper111/

Documentation is still under development so if you want to try it out 
don't hesitate to ask qs.

-r

On Wed, 19 Jul 2006, James W. MacDonald wrote:

> Hi Yen-Tsung,
>
> Yen Tsung Huang wrote:
>> Dear Sir/Madam,     I'm now working on data from Affymetrix 250K Nsp
>> SNParray. My
>> question is: can I use package of RLMM to analyze 250K Nsp array
>> since it mentions RLMM is for 100K Xba array? If not, is there other
>> ways I can use to accommodate the data from 250K Nsp to RLMM, i.e.
>> filter the genes? Or, is there any package can be used for 250K Nsp
>> array? There is a algorithm called BRLMM, modified version of RLMM.
>> Is this new algorithm(BRLMM) served as a new package now?     Thank you
>> very much.
>
> The oligo package has some functions to deal with these chips, but is in
> a developmental stage right now. In addition, you will need a 64 bit
> operating system and lots of RAM to work with any number of these chips.
>
> As for BRLMM, this method AFAIK is only implemented currently in
> software that you can get from Affymetrix. If it is anything like their
> EXACT software you will need to do some work to get it set up, and it
> will likely require lots of RAM as well.
>
> Best,
>
> Jim
>
>
>>
>> Sincerely, Yen-Tsung
>>
>> 	[[alternative HTML version deleted]]
>>
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>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
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>
>
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