[BioC] Summarizing Single-channel Agilent data

[David Westergaard]

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