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Question: questions about RLMM
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gravatar for Yen Tsung Huang
11.4 years ago by
Yen Tsung Huang10 wrote:
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ADD COMMENTlink modified 11.4 years ago by James W. MacDonald45k • written 11.4 years ago by Yen Tsung Huang10
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gravatar for James W. MacDonald
11.4 years ago by
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James W. MacDonald45k 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.
ADD COMMENTlink written 11.4 years ago by James W. MacDonald45k
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 >
ADD REPLYlink written 11.3 years ago by Rafael A. Irizarry2.3k
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