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

[Boris Umylny]

Dear Alex,

Thank you very much for your kind reply.

The RG.MA function is exactly what we were looking for.  I am sorry to trouble 
you with such a trivial question.

Thank you again.


Sincerely,


Boris Umylny


On Thursday 29 January 2009 05:57:03 pm Axel.Klenk at actelion.com wrote:
> Dear Boris,
>
> see ?RG.MA from limma or the RG.MA code for computing normalized RG from
> MA, i.e.
>
> > RG.MA
>
> 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>
>
> Cheers,
>
>  - axel
>
>
> Axel Klenk
> Research Informatician
> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
> Switzerland
> phone +41 61 565 6367 / fax +41 61 565 6470 / axel.klenk at actelion.com /
> www.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 At this point, the two channel data has been replaced by a single value.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?
>
>
> Sincerely,
>
>
> Boris Umylny
>
>
>
>
>
>              [[alternative HTML version deleted]]
>
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