what is the correct way of normalizing 3 different U133 platforms using RMA?
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Jack Luo ▴ 440
@jack-luo-4241
Last seen 9.6 years ago
I have a bunch of cel files profiled on U133A, U133A2 and U133plus2. Obviously, in order to combine them, I'll only focus on the common probes shared by the 3 different platforms. However, I am not sure what is the correct way of RMA normalizing them. Should cel files from the same platform RMA normalized separately, or they can be RMA normalized by only focusing on the common probe sets? Thanks, -Jack [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 15 hours ago
United States
An almost identical question was asked and answered today, so I would point you to the archives: https://stat.ethz.ch/pipermail/bioconductor/2011-August/040726.html Best, Jim On 8/15/2011 3:09 PM, Jack Luo wrote: > I have a bunch of cel files profiled on U133A, U133A2 and U133plus2. > Obviously, in order to combine them, I'll only focus on the common probes > shared by the 3 different platforms. However, I am not sure what is the > correct way of RMA normalizing them. Should cel files from the same platform > RMA normalized separately, or they can be RMA normalized by only focusing on > the common probe sets? > > Thanks, > > -Jack > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Excellent, thanks a bunch! -Jack On Mon, Aug 15, 2011 at 3:16 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > An almost identical question was asked and answered today, so I would point > you to the archives: > > https://stat.ethz.ch/**pipermail/bioconductor/2011-**August/040726.h tml<https: stat.ethz.ch="" pipermail="" bioconductor="" 2011-august="" 040726.htm="" l=""> > > Best, > > Jim > > > > > On 8/15/2011 3:09 PM, Jack Luo wrote: > >> I have a bunch of cel files profiled on U133A, U133A2 and U133plus2. >> Obviously, in order to combine them, I'll only focus on the common probes >> shared by the 3 different platforms. However, I am not sure what is the >> correct way of RMA normalizing them. Should cel files from the same >> platform >> RMA normalized separately, or they can be RMA normalized by only focusing >> on >> the common probe sets? >> >> Thanks, >> >> -Jack >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ************************************************************ > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]
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