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 [[alternative HTML version deleted]]

Hi, The package altcdfenvs was written for such use-cases. Best, L. 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor