[BioC] Limma: Question about extracting 2-channel data

Axel.Klenk at Actelion.Com Axel.Klenk at Actelion.Com
Thu Jan 29 09:57:03 CET 2009

Dear Boris,

see ?RG.MA from limma or the RG.MA code for computing normalized RG from
MA, i.e.

function (object)
    object$R <- 2^(object$A + object$M/2)
    object$G <- 2^(object$A - object$M/2)
    object$M <- NULL
    object$A <- NULL
    new("RGList", unclass(object))
<environment: namespace:limma>


 - axel

Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
phone +41 61 565 6367 / fax +41 61 565 6470 / axel.klenk at actelion.com /

             Boris Umylny                                                  
             <umylny at apbri.org                                             
             >                                                          To 
             Sent by:                  bioconductor at stat.math.ethz.ch      
             bioconductor-boun                                          cc 
             ces at stat.math.eth                                             
             z.ch                                                  Subject 
                                       [BioC] Limma: Question about        
                                       extracting 2-channel data           
             29.01.2009 09:33                                              

Thank you in advance for your help.

We are trying to use limma package to extract and normalize Agilent
2-channel data.  Our objective is to use a single 2-channel chip as 2
1-channel chips.

We attempted the following:

> library(limma)
> targets <- readTargets("targets_file", row.names = "Name")
> RG <- read.maimages(...)
> RG.c <- backgroundCorrect(...)

At this point we have an RG and RG.c objects that contains information for
both channels.

> MA <- normalizeWithinArrays(...)

At this point, the two channel data has been replaced by a single value.

We tried to use targetsA2C to convert to 1-channel design:

> targets.1 <- targetsA2C(targets)
> RG <- read.maimages(targets.1 ...)

However, that simply duplicated Red and Green values.  For 3 chips we had a
set of 3 red and 3 green duplicates.  So, once we get to:

> MA <- normalizeWithinArrays(...)

We have 6 values, but these 6 values are 3 sets of duplicates.

How would we go about getting a set of normalized values from each channel
of a 2-channel chip using limma?


Boris Umylny

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