Change M-value calculation from red/green to green/red

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Torsten Waldminghaus ▴ 80

@torsten-waldminghaus-3502

Last seen 9.7 years ago

Dear all, I started using the limma library to deal with microarray data. The available functions are really helpful to do normalization like this: RG <- read.maimages(files,"agilent") RG.b <- backgroundCorrect(RG,method="minimum") MA.p <-normalizeWithinArrays(RG.b,method="loess") MA.pAq <- normalizeBetweenArrays(MA.p, method="Aquantile") However, in my experiments I had the reference sample labeled in green so I would like to have M-values calculated as M=log2G-log2R instead of M=log2R-log2G. Is there any simple way to do this? Thanks for any help, Torsten Torsten Waldminghaus Department of Cell Biology Institute for Cancer Research Rikshospitalet-Radiumhospitalet-HF Ullernchaussen 70 0310 Oslo tel: 47-22935973 fax: 47-22934580 e-mail: Torsten.Waldminghaus@rr-research.no http://openwetware.org/wiki/User:Torsten_Waldminghaus [[alternative HTML version deleted]]

Microarray Normalization Cancer limma Microarray Normalization Cancer limma • 1.2k views

ADD COMMENT • link updated 14.9 years ago by michael watson IAH-C ★ 3.4k • written 14.9 years ago by Torsten Waldminghaus ▴ 80

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michael watson IAH-C ★ 3.4k

@michael-watson-iah-c-378

Last seen 9.7 years ago

Multiply by -1 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Torsten Waldminghaus Sent: 10 June 2009 10:59 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Change M-value calculation from red/green to green/red Dear all, I started using the limma library to deal with microarray data. The available functions are really helpful to do normalization like this: RG <- read.maimages(files,"agilent") RG.b <- backgroundCorrect(RG,method="minimum") MA.p <-normalizeWithinArrays(RG.b,method="loess") MA.pAq <- normalizeBetweenArrays(MA.p, method="Aquantile") However, in my experiments I had the reference sample labeled in green so I would like to have M-values calculated as M=log2G-log2R instead of M=log2R-log2G. Is there any simple way to do this? Thanks for any help, Torsten Torsten Waldminghaus Department of Cell Biology Institute for Cancer Research Rikshospitalet-Radiumhospitalet-HF Ullernchaussen 70 0310 Oslo tel: 47-22935973 fax: 47-22934580 e-mail: Torsten.Waldminghaus at rr-research.no http://openwetware.org/wiki/User:Torsten_Waldminghaus [[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

ADD COMMENT • link 14.9 years ago michael watson IAH-C ★ 3.4k

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Thanks for helping with this complex mathematical problem :-) -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of michael watson (IAH-C) Sent: 10. juni 2009 12:07 To: Torsten Waldminghaus; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Change M-value calculation from red/green to green/red Multiply by -1 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Torsten Waldminghaus Sent: 10 June 2009 10:59 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Change M-value calculation from red/green to green/red Dear all, I started using the limma library to deal with microarray data. The available functions are really helpful to do normalization like this: RG <- read.maimages(files,"agilent") RG.b <- backgroundCorrect(RG,method="minimum") MA.p <-normalizeWithinArrays(RG.b,method="loess") MA.pAq <- normalizeBetweenArrays(MA.p, method="Aquantile") However, in my experiments I had the reference sample labeled in green so I would like to have M-values calculated as M=log2G-log2R instead of M=log2R-log2G. Is there any simple way to do this? Thanks for any help, Torsten Torsten Waldminghaus Department of Cell Biology Institute for Cancer Research Rikshospitalet-Radiumhospitalet-HF Ullernchaussen 70 0310 Oslo tel: 47-22935973 fax: 47-22934580 e-mail: Torsten.Waldminghaus at rr-research.no http://openwetware.org/wiki/User:Torsten_Waldminghaus [[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 _______________________________________________ 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 REPLY • link 14.9 years ago Torsten Waldminghaus ▴ 80

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