[Bioc-devel] Common workflow to build an microarray annatation package, like hgu133a.db
James W. MacDonald
jmacdon at uw.edu
Wed Jan 6 02:11:52 CET 2016
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.
> 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
> > 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
> > though there are some mappings, such as
> > .
> > Regards,
> > Zhilong
> > --
> > Zhilong JIA
> > zhilongjia at gmail.com
> > https://github.com/zhilongjia
> > [[alternative HTML version deleted]]
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