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?