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

[Sophie Gallina]

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}}
>>>
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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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