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

Fri Aug 17 14:47:00 CEST 2007

Great! 

> -----Original Message-----
> From: Sophie Gallina [mailto:sfi at good.ibl.fr] 
> Sent: 17 August 2007 13:40
> To: Crispin Miller; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Problem with some exonmap X.to.Y functions
> 
> Hi Crispin,
> 
> Your are rigtht.
> I have had some problems during FTP transfert, so many data 
> tables were missing.
> After all ensembl tables installation, plot.gene and all 
> X.to.Y function from exonmap work fine.
> Thanks,
> Sophie
> 
> Crispin Miller a écrit :
> 
> >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}}
> >>>
> >>>_______________________________________________
> >>>Bioconductor mailing list
> >>>Bioconductor at stat.math.ethz.ch
> >>>https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>>Search the archives: 
> >>>http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>
> >>> 
> >>>
> >>>      
> >>>
> >>--
> >>-------------------------------------------------------------------
> >>Sophie.Gallina at good.ibl.fr
> >>CNRS UMR 8090 - http://www-good.ibl.fr Génomique et physiologie 
> >>moléculaire des maladies métaboliques I.B.L - 1 rue du Pr Calmette, 
> >>B.P.245, 59019 Lille Cedex Tel : 33 (0)3.20.87.10.71 Fax : 33 
> >>(0)3.20.87.10.31
> >>
> >>
> >>    
> >>
> > 
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> 
> --
> -------------------------------------------------------------------
> Sophie.Gallina at good.ibl.fr
> CNRS UMR 8090 - http://www-good.ibl.fr
> Génomique et physiologie moléculaire des maladies 
> métaboliques I.B.L - 1 rue du Pr Calmette, B.P.245, 59019 
> Lille Cedex Tel : 33 (0)3.20.87.10.71 Fax : 33 (0)3.20.87.10.31
> 
>

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