Question: RMA, RefRMA questions
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gravatar for James Anderson
12.5 years ago by
James Anderson820 wrote:
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ADD COMMENTlink modified 12.5 years ago by Kuhn, Max70 • written 12.5 years ago by James Anderson820
Answer: RMA, RefRMA questions
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gravatar for Kuhn, Max
12.5 years ago by
Kuhn, Max70
Kuhn, Max70 wrote:
James, >From the presentation that I saw on refRMA (and the paper), the quantile normalization process would coerce the distribution of the low-level probe data to have the same shape as the "reference" data. In GeneLogic's case, they used sets of biological samples from their large data base to define this reference distribution. Assuming that the reference distribution used is acceptable for your samples/problem, this should remove many of the systematic effects that you may have in your data. After googling, it seems that the package is only available form the authors at this time, so I can't be exact. As I mentioned earlier today, I have similar code that I'd be willing to share. It works very similar to the affy RMA functions. Max -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James Anderson Sent: Wednesday, March 07, 2007 3:10 PM To: bioconductor Subject: [BioC] RMA, RefRMA questions Hi, I roughly understand the issue of RMA and RefRMA. When using RefRMA, one RMA model is generated first based on the samples from one lab. If some additional arrays measured in a different lab needs to be normalized, does RefRMA automatically take care of the systematic difference between the two labs or except RefRMA, there are still some extra work needs to be done to correct the systematic difference between the two labs? Thanks, James --------------------------------- The fish are biting. [[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 ---------------------------------------------------------------------- LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
ADD COMMENTlink written 12.5 years ago by Kuhn, Max70
Kuhn, Max wrote: > After googling, it seems that the package is only available form the > authors at this time, so I can't be exact. This package is part of BioC devel: http://bioconductor.org/packages/2.0/bioc/html/RefPlus.html It can be installed directly using biocLite() if you are running R-2.5.0devel. Best, Jim -- 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 REPLYlink written 12.5 years ago by James W. MacDonald51k
So there is no refRMA method. They are called RMA+ and RMA++. I can't wait for RMA#. Thanks, Max -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Wednesday, March 07, 2007 4:09 PM To: Kuhn, Max Cc: James Anderson; bioconductor Subject: Re: [BioC] RMA, RefRMA questions Kuhn, Max wrote: > After googling, it seems that the package is only available form the > authors at this time, so I can't be exact. This package is part of BioC devel: http://bioconductor.org/packages/2.0/bioc/html/RefPlus.html It can be installed directly using biocLite() if you are running R-2.5.0devel. Best, Jim -- 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. ---------------------------------------------------------------------- LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
ADD REPLYlink written 12.5 years ago by Kuhn, Max70
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