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Exon-Level Normalization From Affymetrix Mogene 1.1 St

I need to normalize data from the Affymetrix Mouse Gene 1.1 ST array to produce expression calls by exon. I currently get gene-level calls using oligo:

library(oligo)
celFiles <- list.celfiles(DIRLOC, full.names = TRUE)
affyExpressionFS <- read.celfiles(celFiles, pkgname = "pd.mogene.1.1.st.v1")
ppData <- rma(affyExpressionFS)

I know I can get probeset-level calls by using the target parameter of oligo's rma(). However, there are usually several probesets per exon on this chip, and I would rather not have to reconstitute this for all genes (e.g., map probesets to exons and create new meta-probesets that are actually exons). When Speed's group did their Affymetrix chip comparison they did exactly this for human data. Has anyone already solved this problem for mouse?

microarray affymetrix exon
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updated by Malachi Griffith Malachi Griffith • written by David Quigley David Quigley

1 answer

You should be able to do this with the Aroma package...

You can obtain a custom CDF file for the MoGene 1.1 ST array and then perform exon-by-exon summarization.

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written by Malachi Griffith Malachi Griffith

Thanks for your answer. I ultimately built my own CDF.

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written by David Quigley David Quigley

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