Problem with some exonmap X.to.Y functions
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@sophie-gallina-2306
Last seen 8.4 years ago
Hi, I have problems with some exonmap functions : I made test for the functions X.to.Y described in the page http://rss.acs.unt.edu/Rdoc/library/exonmap/html/X.toY.html using ensembl ID for TP53 gene. probeset.to.exon and exon.to.probeset work fine, the other functions do not work, that is probeset.to.transcript, probeset.to.gene, exon.to.transcript, exon.to.gene transcript.to.exon, transcript.to.probeset, transcript.to.gene gene.to.exon, gene.to.probeset symbol.to.probeset, symbol.to.gene plot.gene don't work neither. What I am missing ? Thanks, Sophie Gallina Here is the trace of the execution ================================================= R version 2.5.1 (2007-06-27) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R est un logiciel libre livr? sans AUCUNE GARANTIE. Vous pouvez le redistribuer sous certaines conditions. Tapez 'license()' ou 'licence()' pour plus de d?tails. R est un projet collaboratif avec de nombreux contributeurs. Tapez 'contributors()' pour plus d'information et 'citation()' pour la fa?on de le citer dans les publications. Tapez 'demo()' pour des d?monstrations, 'help()' pour l'aide en ligne ou 'help.start()' pour obtenir l'aide au format HTML. Tapez 'q()' pour quitter R. > library(exonmap) Le chargement a n?cessit? le package : affy Le chargement a n?cessit? le package : Biobase Le chargement a n?cessit? le package : tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Le chargement a n?cessit? le package : affyio Le chargement a n?cessit? le package : simpleaffy Le chargement a n?cessit? le package : genefilter Le chargement a n?cessit? le package : survival Le chargement a n?cessit? le package : splines Le chargement a n?cessit? le package : RColorBrewer Le chargement a n?cessit? le package : RMySQL Le chargement a n?cessit? le package : DBI Le chargement a n?cessit? le package : plier > xmapDatabase("Human") Switching to human database... done. > # the probeset 3102398 is in TP53 gene > # ENSG00000141510 : ensembl gene ID for TP53 > # ENST00000269305 : one of the ensembl Transcript ID for TP53 > # ENSE00000697174 : one of the ensembl exon ID for TP53 > > # the 2 next functions are OK > probeset.to.exon("3102398") [1] "ENSE00000697174" > exon.to.probeset("ENSE00000697174") [1] "3102398" > > # next ones don't work > probeset.to.transcript("3102398"); [1] NA > probeset.to.gene("3102398"); [1] NA > exon.to.transcript("ENSE00000697174") [1] NA > exon.to.gene("ENSE00000697174") [1] NA > transcript.to.exon("ENST00000269305") NULL > transcript.to.probeset("ENST00000269305") NULL > transcript.to.gene("ENST00000269305") NULL > gene.to.exon("ENSG00000141510") NULL > gene.to.probeset("ENSG00000141510") NULL > symbol.to.probeset("TP53", db=c("hugo","symbol","UniProt","RefSeqPeptide","RFAM","UniProtSpliceVa riant","miRNA")) NULL > symbol.to.gene("TP53") NULL > > plot.gene("ENSG00000141510") Erreur dans apply(all.probes[all.probes[, 5] != 1, ], 1, function(p) { : dim(X) doit avoir un longueur positive Ex?cution arr?t?e -- ------------------------------------------------------------------- Sophie.Gallina at good.ibl.fr CNRS UMR 8090 - http://www-good.ibl.fr G?nomique et physiologie mol?culaire des maladies m?taboliques 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
exonmap exonmap • 1.1k views
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 8.4 years ago
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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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 8.4 years ago
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> > 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 ?crit : > > >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 > G?nomique et physiologie mol?culaire des maladies > m?taboliques 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 > > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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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 ?crit : >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> >>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 ?crit : >> >> >> >>>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 >>G?nomique et physiologie mol?culaire des maladies >>m?taboliques 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 >> >> >> >> > >-------------------------------------------------------- > > >This email is confidential and intended solely for the use ...{{dropped}}
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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 ?crit : > > >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> > >>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 ?crit : > >> > >> > >> > >>>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 G?nomique et physiologie > >>mol?culaire des maladies m?taboliques 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 > >> > >> > >> > >> > > > >-------------------------------------------------------- > > > > > >This email is confidential and intended solely for the use > of the person(s) ('the intended recipient') to whom it was > addressed. Any views or opinions presented are solely those > of the author and do not necessarily represent those of the > Paterson Institute for Cancer Research or the University of > Manchester. It may contain information that is privileged & > confidential within the meaning of applicable law. > Accordingly any dissemination, distribution, copying, or > other use of this message, or any of its contents, by any > person other than the intended recipient may constitute a > breach of civil or criminal law and is strictly prohibited. > If you are NOT the intended recipient please contact the > sender and dispose of this e-mail as soon as possible. > > > > > > > > > > > -- > ------------------------------------------------------------------- > Sophie.Gallina at good.ibl.fr > CNRS UMR 8090 - http://www-good.ibl.fr > G?nomique et physiologie mol?culaire des maladies > m?taboliques 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 > > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
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