[BioC] annotations for Codelink arrays

[Weiwei Shi]

Hi, everyone:

Last time I used Unigene and biomaRt to annotate the probes from rat
codelink to human entrezgene for my research and this time I would
like to try to use GEOQuery, r10kcod and rnohomology. I will compare
the two results.

Thanks for the great work to build those packages.

Weiwei

On 4/5/07, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> Weiwei Shi wrote:
> > Hi, there:
> > I am analyzing an expression profile using CodeLink RU1 arrays and
> > assume I could use the package called r10kcod for annotation. I did
> > some manual work before by using biomaRt and now I would like to try
> > this package. I searched the archives and found the following old post
> > (on 2005), discussing on a couple of issues like one2multiple mapping.
> > Here I am wondering how these problems have been solved in this new(?)
> > package.
> >
> Hi, Weiwei.  I'm not sure which problem you mean--the one-to-many
> probe-to-gene mapping or the way it is handled by the annotation
> package.  If you install the package and look at the r10kcodENTREZID
> environment, it looks like there are 7864 probes with Entrez Gene IDs,
> and there is only one Gene ID per probe in every case.  If you want to
> know if that is "correct" for your needs, you will probably want to
> investigate some of the probes by hand.  However, I tend to do this
> after doing all my analysis with the final gene list, since then you
> know which probes are most important to your hypothesis.  For codelink
> arrays, do you have the sequence of the probes?  If so, it is pretty
> easy to put some of those sequences into NCBI Blast to see what the
> probes would be predicted to hybridize against.
>
> Sean
>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III