[BioC] How to make the probe package for gcrma?
James W. MacDonald
jmacdon at med.umich.edu
Fri Mar 7 15:17:18 CET 2008
Jun Yin wrote:
> 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:
Also note that these are all hosted by BioC as well, so you can install
using the canonical installation:
which will get you the Entrez Gene based cdf and probe packages.
> Jun Yin
> Ph.D. candidate in U.C.D.
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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