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@stat.math.ethz.ch on behalf of marco fabbri
Sent: Fri 11/24/2006 10:21 AM
To: Steffen Durinck
Cc: bioconductor@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@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@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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