[BioC] Problem with some exonmap X.to.Y functions

[Crispin Miller]

Hi Sophie,
Transcript, transcript_attrib, and transcript_stable_id should all have (a lot) of data in them. Looking at your row counts, you seem to be missing various bits of Ensembl - as you suggest, it looks like something seems to have gone wrong in the Ensembl install. 

Can I suggest that the first thing to try is a clean re-install of Ensembl and then X:MAP. 
cheers,

Crispin




> -----Original Message-----
> From: Sophie Gallina [mailto:sfi at good.ibl.fr] 
> Sent: 14 August 2007 17:14
> To: Crispin Miller; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Problem with some exonmap X.to.Y functions
> 
> Hi,
> 
> Thanks for you answer.
> 
> I have installed exonmap 1.0.06 now, but I get the same 
> messages (even for plot.gene).
> I use exon.pmcdf version 1.1 (lastest one, dowloaded from
> http://xmap.picr.man.ac.uk/downloads/exon.pmcdf_1.1.tar.gz)
> </downloads/exon.pmcdf_1.1.tar.gz>
> I have installed ensembl homo_sapiens_core_45_36g and 
> homo_sapiens_otherfeatures_45_36g then X:MAP 
> xmap_homo_sapiens_core_45_36g and homo_sapiens_otherfeatures_45_36g
> 
> I first suspected that the problem could come from the SQL 
> stored procedures, so I tested these procedures directly from  mysql.
> I have attached the sql script (check_stored_proc.sql) and 
> the output file (check_stored_proc.out) Could you please run 
> this sql script on your server and send me back the output ?
> mysql --database=homo_sapiens_core_45_36g  --user=USER 
> --password=PASSWD < check_stored_proc.sql I thinks that some 
> data are missing on my server because :
> some functions returns valid data (eg xmap_probesetToExon) 
> other returns records with only NULL fields (for example
> xmap_probesetToGene)
> others returns no records (eg xmap_geneToExon)
> 
> by the way, mysqld version is :
> /usr/sbin/mysqld --version
> /usr/sbin/mysqld  Ver 5.0.24a-log for mandriva-linux-gnu on 
> x86_64 (Mandriva Linux - MySQL Standard Edition (GPL))
> 
> So I suspected that some data are simply not in the mysql 
> database (perhaps due to a problem during data importation) I 
> check that the number of records in each table = the number 
> of line from table.sql file in ensembl and xmap distribution.
> But the count was OK (see attached file mysql_count.xls).
> However, Is it OK that tables such as transcript, 
> transcript_attrib and transcript_stable_id have no record at 
> all ? is that the same on your server ?
> 
> Thanks for your help,
> sophie Gallina
> 
> 
> Crispin Miller a écrit :
> 
> >Hi Sophie,
> >Taking the last bit first - the bug in plot gene you have has been 
> >fixed
> >- please can you update exonmap to version 1.0.06.
> >
> >---
> >As far as the other problems you were having, I'm a bit confused... 
> >What version of the X:MAP database are you using - and what 
> version of 
> >Ensembl?
> >
> >I've just checked things on our installation here:
> >
> >Using exonmap (and corresponding Ensembl download) version:
> >homo_sapiens_core_45_36g
> >
> >I get:
> >
> >  
> >
> >>probeset.to.exon("3102398")
> >>    
> >>
> >[1] "ENSE00000697174"
> >  
> >
> >>exon.to.probeset("ENSE00000697174")
> >>    
> >>
> >[1] "3102398"
> >  
> >
> >>probeset.to.transcript("3102398");
> >>    
> >>
> >[1] "ENST00000260128"
> >  
> >
> >>probeset.to.gene("3102398");
> >>    
> >>
> >[1] "ENSG00000137573"
> >
> >
> >But...
> >According to X:MAP, '3102398' is a probeset targeting SULF1, 
> not TP53:
> >
> >http://xmap.picr.man.ac.uk/#8/70650974/15/h
> >
> >Again, "ENSG00000137573" is SULF1 and ENST00000260128 and
> >ENSE00000697174 are both transcripts and exons within that genem and 
> >the
> >probeset->exon->transcript->gene hierarchy is what you would expect.
> >
> >I won't post the full output of testing, but I get sensible answers 
> >back for the rest of your queries too.
> >
> >Crispin
> > 
> >--------------------------------------------------------
> >
> > 
> >This email is confidential and intended solely for the use 
> >o...{{dropped}}
> >
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> >
> >  
> >
> 
> 
> --
> -------------------------------------------------------------------
> Sophie.Gallina at good.ibl.fr
> CNRS UMR 8090 - http://www-good.ibl.fr
> Génomique et physiologie moléculaire des maladies 
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