[BioC] exonmap RMA function

[Crispin Miller]

Hi, 
Did you install the whole Ensembl Homo_spaiens core database before you
installed X:Map? 

We don't use all the tables in Ensembl but it is complex enough to make it
generally easier just to install the whole database rather than to try to
install bits of it.

Crispin






On 22/1/08 02:39, "Yuan Jian" <jayuan2008 at yahoo.com> wrote:

> Hi Crispin,
> 
> 1/
> I installed xmap database in my localhost.
> but when I ask for transcript for a probeset. it always returns NULL or NA.
> 
>> xmapDatabase("Human")
> done.
>> probeset.to.transcript("3102379")
> [1] NA
>> probeset.to.transcript("1112997")
> NULL
>> probeset.to.transcript("3933543")
> [1] NA
>> probeset.to.transcript("3102411")
> [1] NA
>> probeset.to.transcript("3102443")
> [1] NA
>> probeset.to.transcript("2315101")
> NULL
> 
> for the function of probe.to.transcript, which tables in
> xmap_homo_sapiens_core_47_36i have been used?
> 
> 2/ 
> in mysql database, I found probeset_id=1427856 has 7120 probes.
> does this probeset has really so many probes?
> in R I can not find probes for this probeset as below:
> 
>> probeset.to.probe("1427856")
> NULL
> 
> is there anything wrong in my installation or using?
> 
> thanks
> Yuan
> 
> 
> 
> ----- Original Message ----
> From: Crispin Miller <CMiller at picr.man.ac.uk>
> To: Jay an <jayuan2007 at yahoo.com>
> Cc: Bioconductor <bioconductor at stat.math.ethz.ch>
> Sent: Tuesday, January 22, 2008 1:19:49 AM
> Subject: Re: [BioC] exonmap RMA function
> 
> 
> Hi,
> If you have a copy of the X:Map database installed and exonmap set up
> properly, then a call to probeset.to.transcript(X), where X is a list
>  of
> probeset ids, will give you a transcript list back...
> 
> See ?probeset.to.transcript and the vignette for more details...
> 
> cheers
> Crispin
> 
> 
> 
> 
> 
> On 21/1/08 11:41, "Jay an" <jayuan2007 at yahoo.com> wrote:
> 
>> Martin, Thanks.
>> the corresponding between probeset and probe can be obtained by using
>> mget(featurenames(x.rma), exon.pmcdf). my another question is:
>> is there a way to get corresponding between transcripts
>> and probesets?
>> 
>> thanks
>> Yuan
>> 
>> 
>  
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