[BioC] biomart scripting help

[Steffen Durinck]

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
>
> _______________________________________________
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>


-- 
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
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