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

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 _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com