[BioC] Re-annotation of probes for an Affy custom microarray

Laurent Gautier laurent at cbs.dtu.dk
Tue Jun 21 08:14:45 CEST 2011


The package altcdfenvs was written for such use-cases.



On 2011-06-21 01:19, Ariel Grostern wrote:
> Hello,
> I have a custom Affy Genechip that was designed using a draft version of a bacterial genome. We now have the finished version of the genome sequence available, so I would like to re-annotate the microarray probes to reflect the new genome sequence and gene numbering system.
> This problem appears to be something that many groups deal with on a regular basis, and I know that Affy constantly updates its annotation.
> Therefore, I was wondering if anyone could guide me in how I can go about re-annotating my array probes? Perhaps you have a pipeline that would be easily adapted to my probes and genome sequence? I know the basic sequence of events: map probes to new gene set->take list of exact matches->re-group probes->create CDF, but I don't know how to actually achieve these steps.
> Thank you for any help or points you can provide.
> Ariel Grostern
> post-doctoral researcher
> Alvarez-Cohen Lab
> Civil and Environmental Engineering
> UC Berkeley
> arielDOTgrosternATberkeleyDOTedu
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