[BioC] How to make the probe package for gcrma?

[James W. MacDonald]

Hi Jun,

Jun Yin wrote:
> Hi, 
> 
> My research subject focus on investigating zebrafish development using 
> Affymetrix GeneChip.
> 
> I plan to reannotate the Affy Zebrafish Genechip, thus I will create a 
> new cdf file. As indicated in the gcrma package, I need a probe sequence 
> package along with the cdf file. How can I make such probe package? 
> 
> Is there any package in Bioconductor which can help to create a user-customed cdf file and probe file?

The altcdfenvs package can be used to make a custom cdf. If you then 
want a corresponding probe package, you will need to modify the 
tab-delimited probe file that you can get from the Affy website to 
correspond to the custom cdf, and then use the matchprobes package to 
make the probe package.

But I am a bit confused by your terminology. Re-annotating the zebrafish 
chip shouldn't require a different cdf and probe package. My 
interpretation of the term 'annotate' is the mapping of probesets to 
genes (or transcripts). For that task you want the AnnBuilder package.

If you really are after re-mapped cdfs, you might also consider the MBNI 
packages. These packages use the current genome build to map probesets 
to genes or transcripts (based on Entrez Gene, UniGene, RefSeq, etc), 
which might be what you are after. There are also matching probe 
packages for each mapping variant, so all you would need to do is 
install the packages and go.

For more information, please see:

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp

Also note that these are all hosted by BioC as well, so you can install 
using the canonical installation:

source("http://www.bioconductor.org/biocLite.R")
biocLite(c("drzebrafishdrentrezgcdf","drzebrafishdrentrezgprobe"))

which will get you the Entrez Gene based cdf and probe packages.

Best,

Jim

> 
> 
> 
> 
> Jun Yin
> Ph.D. candidate in U.C.D.
> 2008-03-03
> 
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
> 
> 	[[alternative HTML version deleted]]
> 
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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