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

[Tim Triche, Jr.]

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

best,

--t

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
>
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