[Bioc-devel] Common workflow to build an microarray annatation package, like hgu133a.db

Tim Triche, Jr. tim.triche at gmail.com
Wed Jan 6 01:00:19 CET 2016

1) this is a support.bioconductor.org question
2) don't use .db0 packages, you will rue the day you did



On Tue, Jan 5, 2016 at 3:53 PM, Zhilong Jia <zhilongjia at gmail.com> wrote:

> Hello,
> Happy new year.
> What is the common work-flow to build an microarray annotation package,
> like hgu133a.db.
> For some array, there are probe sequences available, then maybe mapping is
> used? While for other situations, how to deal with? If code used by the
> team available, that will be great. Thank you.
> The specific goal is to build new platform annotation packages which are
> not available now from Bioconductor (what I need is just probe to gene
> symbols).
> It seems Bioconductor update the annotation package when a new version
> releasing due to the update of gene symbols.
> BTW, why name it as hgu133a.db instead of GPL96.db (from GEO) in
> Bioconductor? And user have to find the mapping relationship between them,
> though there are some mappings, such as
> https://gist.github.com/seandavi/bc6b1b82dc65c47510c7#file-platformmap-txt
> .
> Regards,
> Zhilong
> --
> Zhilong JIA
> zhilongjia at gmail.com
> https://github.com/zhilongjia
>         [[alternative HTML version deleted]]
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list