[BioC] questions about RLMM

James W. MacDonald jmacdon at med.umich.edu
Wed Jul 19 15:59:21 CEST 2006

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.



> Sincerely, Yen-Tsung
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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