[BioC] annotations for Codelink arrays

[Sean Davis]

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