1/
I followed your instruction to install database.
which was downloaded xmap_homo_sapiens_core_47_36i.tgz 
from your web page http://xmap.picr.man.ac.uk/download/.
is it the whole Ensembl Homo_sapaiens database?

2/
which tables are accessed in function probeset.to.transcript?

regards

Yuan



----- Original Message ----
From: Crispin Miller <CMiller@picr.man.ac.uk>
To: Yuan Jian <jayuan2008@yahoo.com>
Cc: Bioconductor <bioconductor@stat.math.ethz.ch>
Sent: Tuesday, January 22, 2008 7:08:17 PM
Subject: Re: [BioC] exonmap RMA function


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@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@picr.man.ac.uk>
> To: Jay an <jayuan2007@yahoo.com>
> Cc: Bioconductor <bioconductor@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@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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