[BioC] Query regarding entrez id

[Marc Carlson]

Hi Varpal,

What kind of probes are they (what platform)?  Have you read the posting
guide?  A lot of people find it very helpful.

http://www.bioconductor.org/docs/postingGuide.html

If you are trying to match probes to entrez gene Ids you might want to
start by reading the vignettes in AnnotationDbi found here:

http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html

For Arabidopsis, entrez gene Ids can be found in the org.At.tair.db
package.  And, you can map to them by using the TAIR identifiers
presented by the probe package of your choice (from the ACCNUM mapping
in the probe package).  Please let us know if you need further
clarifications.

so for example if you had probe ids from the affy "ag" platform:

library(ag.db)
ids = c("11987_at","11988_at","11989_at")
probeTAIR = toTable(agACCNUM[ids])
merge(probeTAIR, toTable(org.At.tairENTREZID))



  Marc



On 05/11/2010 02:02 AM, Sean Davis wrote:
> On Tue, May 11, 2010 at 2:15 AM, varpal singh <gilvarpal at gmail.com> wrote:
>
>   
>> Hi Sir,,
>>
>> I would like to know about entrez id of arabidopsis, I have probe ids of
>> differential expressed genes, I wan to know about their entrez id by
>> bioconductor, how van i get??
>> Please tell me!!
>>
>>
>>     
> Hi, Varpal.
>
> Please write to the bioconductor email list when asking questions.  You will
> get better answers there and many people can benefit from those answers.
>
> As to your question, you'll need to be more specific about what you have
> done.  In particular, what array are you using?  Also, when asking questions
> on the list, be sure to include the output of sessionInfo().
>
> Sean
>
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