Exon-Level Normalization From Affymetrix Mogene 1.1 St
1
0
Entering edit mode
13.6 years ago

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 • 3.6k views
ADD COMMENT
1
Entering edit mode
12.8 years ago

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 COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1759 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6