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

[James W. MacDonald]

On Jan 5, 2016 7:01 PM, "Tim Triche, Jr." <tim.triche at gmail.com> wrote:
>
> 1) this is a support.bioconductor.org question
> 2) don't use .db0 packages, you will rue the day you did

Can you expand on this statement? Right now all of the ChipDb are built
using a db0 package, so it's not clear to me why this might be a problem.

> 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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> >
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> >
>
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