Question: Exon-Level Normalization From Affymetrix Mogene 1.1 St
gravatar for David Quigley
9.5 years ago by
David Quigley11k
San Francisco
David Quigley11k wrote:

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:

celFiles <- list.celfiles(DIRLOC, full.names = TRUE)
affyExpressionFS <- read.celfiles(celFiles, pkgname = "")
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?

exon microarray affymetrix • 2.8k views
ADD COMMENTlink written 9.5 years ago by David Quigley11k
gravatar for Malachi Griffith
8.6 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

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.

ADD COMMENTlink written 8.6 years ago by Malachi Griffith18k

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

ADD REPLYlink written 8.6 years ago by David Quigley11k
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