[BioC] Summarizing Single-channel Agilent data

[Gordon K Smyth]

Dear David,

What you do mean by "summarizing".  Are you perhaps looking for avereps()?

BTW, the read can be done slightly more succintly by

   RG <- read.maimages(targets,source="agilent.median",green.only=TRUE)

Best wishes
Gordon

> Date: Fri, 2 Mar 2012 15:51:00 +0100
> From: David Westergaard <david at harsk.dk>
> To: bioconductor at r-project.org
> Subject: [BioC]  Summarizing Single-channel Agilent data
>
> 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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