[BioC] Custom CDFs from U mich for GeneChip Analysis

[James W. MacDonald]

Hi Ken,

Lo, Ken wrote:
> Hi all, 
> 
> I just recently came across a paper by Dai et al, Nucleic Acids
> Research, 2005 that talks about transcript definitions of the GeneChip
> arrays being based on old genome builds.  They have in turn reannotated
> the platforms based on specific critieria outlined in the paper.  Has
> anyone tried their custom CDFs?  Also, how would one patch this to use
> with gcrma?

No patch needed. These packages are all available from BioC. There is a 
cdfname argument for all of the functions you might need to use to do an 
analysis that will cause an automatic download and installation of the 
correct package(s).

The package names are a bit cryptic, mainly because they need to 
indicate the species/chip/species used for annotation/database, so for 
instance the annotation package for the HG-U133plus2 chip (annotated to 
Entrez Gene) would have a name like hs133phsentrezg.

You could use these chips like this:

dat <- ReadAffy(cdfname="hs133phsentrezgcdf")
eset <- rma(dat)
gset <- gcrma(dat)

Best,

Jim


> 
> Best regards,
> 
> Ken
>  
> 
> **********************************************
> 
> Ken Lo, PhD
> Post-Doctorate Fellow
> Department of Cancer Genetics
> Center for Genetics and Pharmacology
> Roswell Park Cancer Institute
> Elm and Carlton Streets
> Buffalo, New York 14263
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>  
> Located in the
> Buffalo Life Science Complex
> on the Buffalo Niagara Medical Campus
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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