[BioC] Summarizing Single-channel Agilent data

David Westergaard david at harsk.dk
Fri Mar 2 15:51:00 CET 2012


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

More information about the Bioconductor mailing list