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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >