hi steffen, hi georg,

i have also problems with the getGene function (but in linux fc5). i used
the commands from the vignette to test biomaRt, but got an error in the
getGene call:


> mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
Checking attributes and filters ... ok
> getAffyArrays(mart)
 [1] "affy_hc_g110"        "affy_hg_focus"       "affy_hg_u133a"
 [4] "affy_hg_u133a_2"     "affy_hg_u133b"       "affy_hg_u133_plus_2"
 [7] "affy_hg_u95av2"      "affy_hg_u95b"        "affy_hg_u95c"
[10] "affy_hg_u95d"        "affy_hg_u95e"        "affy_hugenefl"
[13] "affy_u133_x3p"
> upregulated <- c("210708_x_at", "202763_at", "211464_x_at")
> getGene(id = upregulated, array = "affy_hg_u133_plus_2", mart = mart)
Error: ncol(result) == length(attributes) is not TRUE

As the same commands worked on a system running the same linux, R, biomaRt
package, but outside our network (and therefore without a http proxy) i
thought the problems are due to the proxy server. so i tested the following:

> getURL("http://www.biomart.org/biomart/martservice?type=registry")
[1] "<MartRegistry>\n  <virtualSchema name=\"dicty\" visible=\"0\">\n
<MartURLLocation default=\"1\" displayName=\"DICTYBASE (NORTHWESTERN)\"
host=\"www.dictybase.org\" includeDatasets=\"\" martUser=\"\" name=\"dicty\"
path=\"\" port=\"80\" redirect=\"1\" serverVirtualSchema=\"dictyMart\"
visible=\"1\" />\n  </virtualSchema>\n  <virtualSchema name=\"default\"
visible=\"0\">\n    <MartURLLocation default=\"1\" displayName=\"ENSEMBL 39
(SANGER)\" host=\"www.biomart.org\" includeDatasets=\"\" martUser=\"\"
name=\"ensembl\" path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"1\" />\n    <MartURLLocation
default=\"0\" displayName=\"SEQUENCE 39 (SANGER)\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"sequence\"
path=\"/biomart/martservice\" port=\"80\" serverVirtualSchema=\"default\"
visible=\"0\" />\n    <MartURLLocation default=\"0\" displayName=\"SNP 39
(SANGER)\" host=\"www.biomart.org\" includeDatasets=\"\" martUser=\"\"
name=\"snp\" path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"1\" />\n    <MartURLLocation
default=\"0\" displayName=\"VEGA 39 (SANGER)\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"vega\"
path=\"/biomart/martservice\" port=\"80\" serverVirtualSchema=\"default\"
visible=\"1\" />\n    <MartURLLocation default=\"0\" displayName=\"UNIPROT
PROTOTYPE 4-5 (EBI)\" host=\"www.biomart.org\" includeDatasets=\"\"
martUser=\"\" name=\"uniprot\" path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"1\" />\n    <MartURLLocation
default=\"0\" displayName=\"MSD PROTOTYPE 4 (EBI)\" host=\"www.biomart.org\"
includeDatasets=\"\" martUser=\"\" name=\"msd\"
path=\"/biomart/martservice\" port=\"80\" serverVirtualSchema=\"default\"
visible=\"1\" />\n    <MartURLLocation default=\"0\" displayName=\"WORMBASE
CURRENT (CSHL)\" host=\"www.biomart.org\" includeDatasets=\"\" martUser=\"\"
name=\"wormbase\" path=\"/biomart/martservice\" port=\"80\"
serverVirtualSchema=\"default\" visible=\"1\" />\n
</virtualSchema>\n</MartRegistry>\n"

and it worked, so RCurl can connect through the proxy, but what is then the
problem in getGene?
any ideas? maybe Georg has the same problem...

thanks in advance,
best, jo

my settings:
> sessionInfo()
Version 2.3.0 (2006-04-24)
x86_64-unknown-linux-gnu

attached base packages:
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "base"

other attached packages:
 biomaRt    RCurl      XML
 "1.7.3"  "0.6-2" "0.99-7"


On 7/13/06, Georg Otto <georg.otto@tuebingen.mpg.de> wrote:
>
> Hi Steffen,
>
> thanks for your help. I updated to biomaRt 1.7.3 and followed your
> advice. What I got is this:
>
> > mart <- useMart("ensembl")
> > mart<-useDataset("drerio_gene_ensembl", mart)
>
> > getGene(id="Dr.10336.1.S1_at", array="affy_zebrafish", mart=mart)
> NULL
>
> then I tried with getBM
>
> > getBM(attributes=c("ensembl_transcript_id", "affy_zebrafish",
> "refseq_dna"), filters="affy_zebrafish", values="Dr.10336.1.S1_at",
> mart=mart)
> NULL
>
> I tried with several different affymetrix probes that should be
> annotated in ensembl, but all of them gave me a "NULL"
>
> > sessionInfo()
> Version 2.3.0 (2006-04-24)
> x86_64-redhat-linux-gnu
>
> attached base packages:
> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
> [7] "base"
>
> other attached packages:
> biomaRt    RCurl      XML
> "1.7.3"  "0.6-2" "0.99-7"
>
> Any idea what could be wrong here?
>
> Best,
>
> Georg
>
>
> Steffen Durinck <durincks@mail.nih.gov> writes:
>
> > Hi Georg,
> >
> > You need to use the latest version of biomaRt 1.7.3 for getGene to work
> > with zebrafish (See developmental packages).
> > http://www.bioconductor.org/packages/1.9/bioc/html/biomaRt.html
> >
> > Also have a look at the getBM, listAttributes and listFilters
> > functions...these are robust against Ensembl database changes and allow
> > you to query more than what is possible with the simple biomaRt
> > functions such as getGene.
> >
> > Best,
> > Steffen
> >
> > Georg Otto wrote:
> >> Hi,
> >>
> >> I have a problem using biomaRt. I want to retrieve information
> connected to a probe, and do something like this:
> >>
> >>
> >>> mart<-useMart("ensembl", dataset="drerio_gene_ensembl")
> >>>
> >> Checking attributes and filters ... ok
> >>
> >>> getAffyArrays(mart)
> >>>
> >> [1] "affy_zebrafish"
> >>
> >>> getGene(id="Dr.1.1.S1_at", array="affy_zebrafish", mart=mart)
> >>>
> >> Error in getBM(attributes = c(attrib, "hgnc_symbol", "description",
> chrname,  :
> >>      attribute: hgnc_symbol not found, please use the function
> 'listAttributes' to get valid attribute names
> >>
> >>
> >>
> >>> listAttributes(mart=mart)
> >>>
> >>
> >> <snip>
> >>   [8] "adf_swissprot"
> >>   [9] "affy_zebrafish"
> >>  [10] "affy_zebrafish_primary_db"
> >>  [11] "agilent_g2518a"
> >> <snip>
> >>
> >> So it seems that the attribute "affy_zebrafish" exists.
> >>
> >> What is wrong here? I had this problem before, and I got a reply from
> >> Steffen Durinck (see below) that it has to do with an inconistency in
> >> attribute and filter naming, i.e. the attribute for the affyids was
> >> zebrafish_affy and the filter was called affy_zebrafish. I was told
> >> that this will be fixed in the next ensembl release. It seems that the
> >> diffrence between the array and the attribute has been repaired, since
> >> both are now called affy_zebrafish, but the problem still persists.
> >>
> >>
> >>> sessionInfo()
> >>>
> >> Version 2.3.1 (2006-06-01)
> >> powerpc-apple-darwin8.6.0
> >>
> >> attached base packages:
> >> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"
> >> [7] "base"
> >>
> >> other attached packages:
> >>      DBI  biomaRt    RCurl      XML
> >> "0.1-10"  "1.6.0"  "0.6-2" "0.99-7"
> >>
> >> Cheers,
> >>
> >> Georg
> >>
> >>
> >>
> >>
> >>> Hi,
> >>>
> >>>
> >>>> My understanding is that the BioMart folks are making changes to the
> >>>> table names for the BioMart database, and this is happening right now
> >>>> (e.g, right after BioC 1.8 is released). Unfortunately this means
> that
> >>>> some of the convenience functions like getGene() are being broken.
> >>>>
> >>
> >>
> >>
> >>> This is correct however here there is a problem with the zebrafish
> dataset
> >>> as well.  Part of the error here is produced by an inconistency in
> >>> attribute and filter naming.  The attribute for the affyids is
> >>> zebrafish_affy and the filter is called affy_zebrafish.  The getGene
> >>> function expects these to have the same name and thus generates an
> error.
> >>>
> >>> To make the BioMart datasets better we can post these inconsistencies
> to
> >>> the corresponding BioMart mailinglist (in this case the Ensembl
> helpdesk)
> >>> so they get fixed in the next database release.
> >>>
> >>> Best,
> >>> Steffen
> >>>
> >>>
> >>>> Hi Georg,
> >>>>
> >>>> Georg Otto wrote:
> >>>>
> >>>>> Hi,
> >>>>>
> >>>>> using biomaRt, I get an error:
> >>>>>
> >>>>>
> >>>>>
> >>>>>> mart<-useMart("ensembl", dataset= "drerio_gene_ensembl")
> >>>>>> getAffyArrays(mart)
> >>>>>>
> >>>>> [1] "affy_zebrafish"
> >>>>>
> >>>>>
> >>>>>> getGene(id=genes.regulated.mas5, array="affy_zebrafish" ,
> mart=mart)
> >>>>>>
> >>>>> Error in getBM(attributes = c(attrib, "hgnc_symbol", "description",
> >>>>> chrname,  :
> >>>>>         attribute: affy_zebrafish not found, please use the function
> >>>>> 'listAttributes' to get valid attribute names
> >>>>>
> >>>>>
> >>>>> Then I use listAttributes() as requested:
> >>>>>
> >>>>>
> >>>>>
> >>>>>> listAttributes(mart=mart)
> >>>>>>
> >>>>> and get the following output:
> >>>>>
> >>>>> <snip>
> >>>>> [309] "zebrafish_affy"
> >>>>> [310] "zebrafish_affy_primary_db"
> >>>>> <snip>
> >>>>>
> >>>>> using "zebrafish_affy" instead of "affy_zebrafish" does not help,
> >>>>> however:
> >>>>>
> >>>>>
> >>>>>
> >>>>>> getGene(id=genes.regulated.mas5, array="zebrafish_affy" ,
> mart=mart)
> >>>>>>
> >>>>> Error in getBM(attributes = c(attrib, "hgnc_symbol", "description",
> >>>>> chrname,  :
> >>>>>         attribute: hgnc_symbol not found, please use the function
> >>>>> 'listAttributes' to get valid attribute names
> >>>>>
> >>>>> Any hint will be appreciated.
> >>>>>
> >>>> My understanding is that the BioMart folks are making changes to the
> >>>> table names for the BioMart database, and this is happening right now
> >>>> (e.g, right after BioC 1.8 is released). Unfortunately this means
> that
> >>>> some of the convenience functions like getGene() are being broken.
> >>>>
> >>>> I think your best bet is to use getBM() directly, and query for
> things
> >>>> that you see when you do listAttributes(mart).
> >>>>
> >>>> HTH,
> >>>>
> >>>> Jim
> >>>>
> >>
> >> _______________________________________________
> >> 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
> >>
> >
> >
> > --
> > 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
> >
> > _______________________________________________
> > 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
> >
>
> --
>
> Georg Wilhelm Otto
>
> Max-Planck-Institute for Developmental Biology
>
> georg.otto@tuebingen.mpg.de
>
> _______________________________________________
> 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
>



-- 
Johannes Rainer, Msc
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria
Tel.: +43 512 570485 15
Email: johannes.rainer@tcri.at
          johannes.rainer@tugraz.at

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