[BioC] Change M-value calculation from red/green to green/red

[Torsten Waldminghaus]

Thanks for helping with this complex mathematical problem :-)


-----Original Message-----
From: bioconductor-bounces at 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 at 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

 


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