[BioC] CodeLink Probe ID in new Annoation Package different from the NCBI GEO?

[Sean Davis]

On Fri, Mar 14, 2008 at 8:25 PM, Lingsheng Dong <dong_lsh at hotmail.com> wrote:
>
>  Hi, Sean,
> Thank you very much for you response.  I understand your point.
> But the question we are trying to ask is this:
> Because the Array was designed years ago, part of the old annotation
> (GPL1449) should be out of date. If we map the probe sequences to most
> updated RefSeq RNA database and re-analyze the data, we may find some more
> interesting genes. So we don't want use any data from the old annotation
> (GPL1449). In the annotation package h20kcod, probe ID is different from the
> original platform and the expression table. So there is noway to use the
> package.
> If there is not an answer to this problem, could you please tell how I can
> download the probe sequences with the original probe ID?

The bioconductor annotation packages are generally built using
company-supplied annotation; that may have changed, but very well
might not have.  In other words, if the company says that a probe
mapped to NM_000022, then the bioconductor annotation package uses
that RefSeq accession for further lookups.  Generally, no attempt is
made to realign the probes to the newest build of refseq.
Unfortunately, I do not know if you can find or where to find the
probe sequences and original probe IDs.

Sean