[BioC] Summarizing Single-channel Agilent data

[axel.klenk at actelion.com]

Dear David,

AFAIK, summarization is required for short oligo arrays such as Affy's but 
not usually for 
Agilent's 60mer platform. Peeking at the Agi4x44PreProcess vignette (I'm 
not using it 
myself), its summarization is for replicated oligos and not for probesets 
consisting of 
different probes. I think limma's avereps() function will do what you 
want, see ?avereps.

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland




From:
David Westergaard <david at harsk.dk>
To:
bioconductor at r-project.org
Date:
02.03.2012 15:50
Subject:
[BioC]  Summarizing Single-channel Agilent data
Sent by:
bioconductor-bounces at r-project.org



Hello,

I am working on normalizing raw data from
http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-33005 using the
Limma package.

Following "standard" procedure, I do background correction, and then 
normalize:

# Read target from file
targets <- readTargets("targets")
RG <- read.maimages(targets,source="agilent", columns =list(G =
"gMedianSignal", Gb = "gBGMedianSignal"),green.only=TRUE)


# Do backgroundcorrection/normalization
RG <- backgroundCorrect(RG, method="normexp")
RG <- normalizeBetweenArrays(RG, method="quantile")

Now, what I'm lacking is a summarization method. Googling abit,
"Agi4x44PreProcess" can do the summarization, but it doesn't accept
single-channel data. Furthermore, it expects an RGList as input to
summarize.probe (NormalizeBetweenArrays produces an EList)

So how would I go about summarizing these data? It would be nice if
there was an existing package doing this.


Best Regards,
David Westergaard
Undergraduate student
Technical University of Denmark

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