Thank you, this solved my problem. For the second part of my problem. I try to get some annotation on the two lists the starting list (in this example homolog[,1]) and the results list (homolg[,2]) I can use annotation= getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", "chromosome_name", "band"), filters = "affy_hg_u95av2", values = homolog[,1], mart = human) show(annotation) affy_hg_u95av2 hgnc_symbol chromosome_name band 1 1939_at TP53 17 p13.1 ... but I can not to create a single table with cbind(homolog, annotation), I would like to have a NA for gene not founded and for repeated ID, repeated annotation. thanks Marco On 24/11/06, Steffen Durinck <durincks at="" mail.nih.gov=""> wrote: > Hi Marco, > > If you use biomaRt in MySQL mode for this query you will get both the > affy_mouse430_2 and affy_hg_u95av2 ids in the result. > The reason why this doesn't happen in the webservice (default) mode is > that the BioMart webservice currently doesn't allow this, however I > expect this to change in the near future. > > You'll need to install RMySQL, then try: > > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", mysql=TRUE) > mouse=useMart("ensembl", dataset = "mmusculus_gene_ensembl", mysql=TRUE) > homolog = getHomolog( id = c("1939_at","2000_at"), to.array > ="affy_mouse430_2", from.array ="affy_hg_u95av2",from.mart = human, > to.mart = mouse ) > > You should get: > > > homolog > id MappedID > 1 1939_at 1427739_a_at > 2 1939_at 1426538_a_at > 3 2000_at 1428830_at > 4 2000_at 1421205_at > > > Cheers, > Steffen > > > > > > marco fabbri wrote: > > I looking for help on biomRt. > > I am starting from a human affy code list and I would like to have the > > mouse homologue. > > If I am running this script I do not know which probe is homologue to > > > > > >> homolog = getHomolog( id = c("1939_at","2000_at"), to.array = > >> > > "affy_mouse430_2 ", from.array ="affy_hg_u95av2", > > from.mart = human, to.mart = mouse ) > > > > > >> show(homolog) > >> > > V1 > > 1 1427739_a_at > > 2 1426538_a_at > > 3 1428830_at > > 4 1421205_at > > > > I also tried with getBM but no success.. > > My ideal result would be: from a humann affy id list to get a table like that: > > > > human_probesets -- human_gene_name -- homol_mouse_probesets -- > > homolog_mouse_gene_name > > > > Thank Marco > > > > _______________________________________________ > > 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 > > > > -- --------------------------------------- Marco Fabbri Istituto Clinico Humanitas via Manzoni, 52 20089 Rozzano (Mi) Tel. 028224 5152 Fax 028224 5101

Hi Ariel, You should have enough by having the MySQL client installed. Did the installation of RMySQL give any errors? Try installing the RMySQL package from command line with R CMD INSTALL. It should tell you which environment variables need to be set to point R to your MySQL client installation. Best, Steffen Ariel Chernomoretz wrote: > > Hi Marco, Steffen, > > I was following your thread, because I want to do the same homology > mapping using biomaRt. > However I am kind of stuck because I could not install RMySql. > It seems that mysql.h is missing in my system. > > I am running a Fedora Core 5 Linux , and I think I have only the > client stuff of mysql. > Should I get the server version installed? Binary or source-and- compiled? > would that interfere with the already installed mysql soft I have here? > > Any help would be appreciated. > Regards > Ariel./ > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of marco fabbri > Sent: Fri 11/24/2006 10:21 AM > To: Steffen Durinck > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] biomart scripting help > > Thank you, > this solved my problem. > For the second part of my problem. > I try to get some annotation on the two lists > the starting list (in this example homolog[,1]) and the results list > (homolg[,2]) > > I can use > annotation= getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", > "chromosome_name", > "band"), filters = "affy_hg_u95av2", values = homolog[,1], mart = human) > show(annotation) > affy_hg_u95av2 hgnc_symbol chromosome_name band > 1 1939_at TP53 17 p13.1 > > ... but I can not to create a single table with cbind(homolog, > annotation), I would like to have a NA for gene not founded and for > repeated ID, repeated annotation. > > thanks Marco > > > > On 24/11/06, Steffen Durinck <durincks at="" mail.nih.gov=""> wrote: > > Hi Marco, > > > > If you use biomaRt in MySQL mode for this query you will get both the > > affy_mouse430_2 and affy_hg_u95av2 ids in the result. > > The reason why this doesn't happen in the webservice (default) mode is > > that the BioMart webservice currently doesn't allow this, however I > > expect this to change in the near future. > > > > You'll need to install RMySQL, then try: > > > > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", > mysql=TRUE) > > mouse=useMart("ensembl", dataset = "mmusculus_gene_ensembl", mysql=TRUE) > > homolog = getHomolog( id = c("1939_at","2000_at"), to.array > > ="affy_mouse430_2", from.array ="affy_hg_u95av2",from.mart = human, > > to.mart = mouse ) > > > > You should get: > > > > > homolog > > id MappedID > > 1 1939_at 1427739_a_at > > 2 1939_at 1426538_a_at > > 3 2000_at 1428830_at > > 4 2000_at 1421205_at > > > > > > Cheers, > > Steffen > > > > > > > > > > > > marco fabbri wrote: > > > I looking for help on biomRt. > > > I am starting from a human affy code list and I would like to have the > > > mouse homologue. > > > If I am running this script I do not know which probe is homologue to > > > > > > > > >> homolog = getHomolog( id = c("1939_at","2000_at"), to.array = > > >> > > > "affy_mouse430_2 ", from.array ="affy_hg_u95av2", > > > from.mart = human, to.mart = mouse ) > > > > > > > > >> show(homolog) > > >> > > > V1 > > > 1 1427739_a_at > > > 2 1426538_a_at > > > 3 1428830_at > > > 4 1421205_at > > > > > > I also tried with getBM but no success.. > > > My ideal result would be: from a humann affy id list to get a > table like that: > > > > > > human_probesets -- human_gene_name -- homol_mouse_probesets -- > > > homolog_mouse_gene_name > > > > > > Thank Marco > > > > > > _______________________________________________ > > > 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 > > > > > > > > > > -- > --------------------------------------- > Marco Fabbri > Istituto Clinico Humanitas > via Manzoni, 52 > 20089 Rozzano (Mi) > Tel. 028224 5152 > Fax 028224 5101 > > _______________________________________________ > 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 > -- Steffen Durinck, Ph.D. Oncogenomics Section Pediatric Oncology Branch National Cancer Institute, National Institutes of Health URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ Phone: 301-402-8103 Address: Advanced Technology Center, 8717 Grovemont Circle Gaithersburg, MD 20877

Hi Ariel, It says: Manually specify the location of the MySQL libraries and the header files and re-run R CMD INSTALL. Did you set these environment variables before trying the installation? Best, Steffen Ariel Chernomoretz wrote: > > Hi, > > This is what I get from R (same things from shell prompt installation) > > > source("http://www.bioconductor.org/biocLite.R") > > biocLite("RMySQL") > Running getBioC version 0.1.8 with R version 2.4.0 > Running biocinstall version 1.9.9 with R version 2.4.0 > Your version of R requires version 1.9 of Bioconductor. > trying URL > 'http://cran.us.r-project.org/src/contrib/RMySQL_0.5-10.tar.gz' > <http: cran.us.r-project.org="" src="" contrib="" rmysql_0.5-10.tar.gz%27=""> > Content type 'application/x-tar' length 142671 bytes > opened URL > ================================================== > downloaded 139Kb > > * Installing *source* package 'RMySQL' ... > creating cache ./config.cache > checking how to run the C preprocessor... cc -E > checking for compress in -lz... yes > checking for getopt_long in -lc... yes > checking for mysql_init in -lmysqlclient... no > checking for mysql.h... no > checking for mysql_init in -lmysqlclient... no > checking for mysql_init in -lmysqlclient... no > checking for mysql_init in -lmysqlclient... no > checking for mysql_init in -lmysqlclient... no > checking for mysql_init in -lmysqlclient... no > checking for /usr/local/include/mysql/mysql.h... no > checking for /usr/include/mysql/mysql.h... no > checking for /usr/local/mysql/include/mysql/mysql.h... no > checking for /opt/include/mysql/mysql.h... no > checking for /include/mysql/mysql.h... no > > Configuration error: > could not find the MySQL installation include and/or library > directories. Manually specify the location of the MySQL > libraries and the header files and re-run R CMD INSTALL. > > > So it seems it is looking for mysql.h, and probably other include > files, that are missing in my system: > > [ariel at LAB309-10 ~]$ locate mysql.h > /usr/share/doc/selinux-policy-2.2.23/html/services_mysql.html > > > [ariel at LAB309-10 ~]$ rpm -ql mysql | grep mysql?h > [ariel at LAB309-10 ~]$ rpm -ql mysql | grep mysql.h > /usr/bin/mysqlcheck > /usr/bin/mysqlshow > /usr/share/man/man1/mysqlshow.1.gz > /usr/share/mysql/hungarian > /usr/share/mysql/hungarian/errmsg.sys > > > best > > Ariel./ > > > > > > -----Original Message----- > From: Steffen Durinck [mailto:durincks at mail.nih.gov] > Sent: Fri 11/24/2006 11:40 AM > To: Ariel Chernomoretz > Cc: marco fabbri; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] biomart scripting help > > Hi Ariel, > > You should have enough by having the MySQL client installed. > Did the installation of RMySQL give any errors? > Try installing the RMySQL package from command line with R CMD INSTALL. > It should tell you which environment variables need to be set to point R > to your MySQL client installation. > > Best, > Steffen > > Ariel Chernomoretz wrote: > > > > Hi Marco, Steffen, > > > > I was following your thread, because I want to do the same homology > > mapping using biomaRt. > > However I am kind of stuck because I could not install RMySql. > > It seems that mysql.h is missing in my system. > > > > I am running a Fedora Core 5 Linux , and I think I have only the > > client stuff of mysql. > > Should I get the server version installed? Binary or > source-and-compiled? > > would that interfere with the already installed mysql soft I have here? > > > > Any help would be appreciated. > > Regards > > Ariel./ > > > > > > > > -----Original Message----- > > From: bioconductor-bounces at stat.math.ethz.ch on behalf of marco fabbri > > Sent: Fri 11/24/2006 10:21 AM > > To: Steffen Durinck > > Cc: bioconductor at stat.math.ethz.ch > > Subject: Re: [BioC] biomart scripting help > > > > Thank you, > > this solved my problem. > > For the second part of my problem. > > I try to get some annotation on the two lists > > the starting list (in this example homolog[,1]) and the results list > > (homolg[,2]) > > > > I can use > > annotation= getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", > > "chromosome_name", > > "band"), filters = "affy_hg_u95av2", values = homolog[,1], mart = > human) > > show(annotation) > > affy_hg_u95av2 hgnc_symbol chromosome_name band > > 1 1939_at TP53 17 p13.1 > > > > ... but I can not to create a single table with cbind(homolog, > > annotation), I would like to have a NA for gene not founded and for > > repeated ID, repeated annotation. > > > > thanks Marco > > > > > > > > On 24/11/06, Steffen Durinck <durincks at="" mail.nih.gov=""> wrote: > > > Hi Marco, > > > > > > If you use biomaRt in MySQL mode for this query you will get both the > > > affy_mouse430_2 and affy_hg_u95av2 ids in the result. > > > The reason why this doesn't happen in the webservice (default) mode is > > > that the BioMart webservice currently doesn't allow this, however I > > > expect this to change in the near future. > > > > > > You'll need to install RMySQL, then try: > > > > > > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", > > mysql=TRUE) > > > mouse=useMart("ensembl", dataset = "mmusculus_gene_ensembl", > mysql=TRUE) > > > homolog = getHomolog( id = c("1939_at","2000_at"), to.array > > > ="affy_mouse430_2", from.array ="affy_hg_u95av2",from.mart = human, > > > to.mart = mouse ) > > > > > > You should get: > > > > > > > homolog > > > id MappedID > > > 1 1939_at 1427739_a_at > > > 2 1939_at 1426538_a_at > > > 3 2000_at 1428830_at > > > 4 2000_at 1421205_at > > > > > > > > > Cheers, > > > Steffen > > > > > > > > > > > > > > > > > > marco fabbri wrote: > > > > I looking for help on biomRt. > > > > I am starting from a human affy code list and I would like to > have the > > > > mouse homologue. > > > > If I am running this script I do not know which probe is > homologue to > > > > > > > > > > > >> homolog = getHomolog( id = c("1939_at","2000_at"), to.array = > > > >> > > > > "affy_mouse430_2 ", from.array ="affy_hg_u95av2", > > > > from.mart = human, to.mart = mouse ) > > > > > > > > > > > >> show(homolog) > > > >> > > > > V1 > > > > 1 1427739_a_at > > > > 2 1426538_a_at > > > > 3 1428830_at > > > > 4 1421205_at > > > > > > > > I also tried with getBM but no success.. > > > > My ideal result would be: from a humann affy id list to get a > > table like that: > > > > > > > > human_probesets -- human_gene_name -- homol_mouse_probesets -- > > > > homolog_mouse_gene_name > > > > > > > > Thank Marco > > > > > > > > _______________________________________________ > > > > 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 > > > > > > > > > > > > > > > > -- > > --------------------------------------- > > Marco Fabbri > > Istituto Clinico Humanitas > > via Manzoni, 52 > > 20089 Rozzano (Mi) > > Tel. 028224 5152 > > Fax 028224 5101 > > > > _______________________________________________ > > 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 > > > > > -- > Steffen Durinck, Ph.D. > > Oncogenomics Section > Pediatric Oncology Branch > National Cancer Institute, National Institutes of Health > URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ > > Phone: 301-402-8103 > Address: > Advanced Technology Center, > 8717 Grovemont Circle > Gaithersburg, MD 20877 > -- Steffen Durinck, Ph.D. Oncogenomics Section Pediatric Oncology Branch National Cancer Institute, National Institutes of Health URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ Phone: 301-402-8103 Address: Advanced Technology Center, 8717 Grovemont Circle Gaithersburg, MD 20877