[BioC] Annotate Package: How do I get the gene names and how do I write my matrix

[Sean Davis]

On Aug 19, 2004, at 6:36 AM, Adaikalavan Ramasamy wrote:

> See comments below.
>
> On Wed, 2004-08-18 at 18:54, S Peri wrote:
>>
>> Using annotation package how can I convert the probe
>> ID's to Gene names. how do i incorporate gene name in
>> place of 100_g_at?
>>
>
> There are annotation packages in BioConductor. But if you want a
> quick and dirty solution, get the CDF file from affymetrix and
> merge it in excel. These will have all the information you need
> but may be slightly outdated.
>
> Can anyone on the list comment the merits of doing this
> versus using the BioConductor annotation package ?
>

The annotation packages contain much more information than just the 
gene name (like gene ontology, homologous genes, etc.).  If one has a 
vector of affy IDs from, for example, the hgu95av2 chip, getting the 
gene symbol is as simple as:

getSYMBOL(myaffyids,"hgu95av2")

See ?getSYMBOL for more help on getting ids of various types from the 
affy identifiers.

Also, many of the other packages (GOstats, ontoTools, etc.) make 
extensive use of the annotation packages, so, while the "quick and 
dirty" approach will give you simple information, it does pay off if 
one is going to do post-processing of results in R to learn how to use 
the annotation packages.  If all one needs is a gene name, either way 
works (but I still think the annotation package is a more robust 
solution).

Sean