Hi Steffen,

 one more question: In the example i reported before seems like some probes
are reported twice,
i.e. 207893_at is listed 2 times matched to the same gene ID. Totally the
"probes" vector contains the probes from hgu133plus2 (54675) but the query
returns 66565 rows.

I do not understand really the meaning of this ..

Regards

Marco

probe.list       <-
getBM(attributes=c("ensembl_gene_id","affy_hg_u133_plus_2"),filters="affy_hg_u133_plus_2",
values=probes, mart=mart)

head(probes.list)

  ensembl_gene_id affy_hg_u133_plus_2
1 ENSG00000184895           207893_at
2 ENSG00000184895           207893_at
3 ENSG00000129824           201909_at
4 ENSG00000129824           201909_at
5 ENSG00000067646         207247_s_at
6 ENSG00000067646           207246_at



On 4/3/07, Steffen Durinck <durincks@mail.nih.gov> wrote:
>
> Hi Marco,
>
> It matches the transcripts and then maps those transcripts to the genes,
> even if you don't include the transcript id in the query.
> To see this you could set attributes =
> c("ensembl_gene_id","ensembl_transcript_id","affy_hg_u133_plus_2") in
> your query.  Also if Ensembl didn't find a match for the affy probe then
> it won't be included in the output and if they find multiple matches
> then all of them will be returned.
>
> For the second part of your question:  No, the ordering is random so
> you'll have reorder  the output with e.g. the match function or loop
> over it.
>
> Cheers,
> Steffen
>
> marco zucchelli wrote:
> > Steffen,
> >
> > Anyway does this procedure match the affy_ID to the specific
> > transcript(s) that that probeset is targetting or does it match to it
> > to a gene and then gets all the available transcripts for the gene?
> >
> > Morover, it seems that the returned values from getBM are not ordered
> > as the input values.
> > Infact, if I use:
> >
> > head(probes)
> > [1] "AFFX-BioB-5_at"  "AFFX-BioB-M_at"  "AFFX-BioB-3_at"
> > "AFFX-BioC-5_at"  "AFFX-BioC-3_at"  "AFFX-BioDn-5_at"
> >
> > probe.list       <-
> >
> getBM(attributes=c("ensembl_gene_id","affy_hg_u133_plus_2"),filters="affy_hg_u133_plus_2",
> > values=probes, mart=mart)
> >
> > head(probes.list)
> >
> >   ensembl_gene_id affy_hg_u133_plus_2
> > 1 ENSG00000184895           207893_at
> > 2 ENSG00000184895           207893_at
> > 3 ENSG00000129824           201909_at
> > 4 ENSG00000129824           201909_at
> > 5 ENSG00000067646         207247_s_at
> > 6 ENSG00000067646           207246_at
> >
> > Is there any rule based on which the probes are ordered by getBM?
> > Or I am doing somethign wrong?
> >
> >
> > Marco
> >
> >
> >
> > On 3/30/07, *Steffen Durinck* <durincks@mail.nih.gov
> > <mailto:durincks@mail.nih.gov>> wrote:
> >
> >     Hi Marco,
> >
> >     You can do this with the biomaRt package (use the devel version, >=
> >     1.9.21) , here's how:
> >
> >     library(biomaRt)
> >     mart=useMart("ensembl", dataset="hsapiens_gene_ensembl")
> >
> getBM(attributes=c("ensembl_gene_id","ensembl_transcript_id","synonymous_snp_count","non_synonymous_snp_count"),
> >     filters="affy_hg_u133_plus_2", values=c("201746_at","231640_at"),
> >     mart=mart)
> >
> >     it will give:
> >
> >     ensembl_gene_id ensembl_transcript_id synonymous_snp_count
> >     non_synonymous_snp_count
> >     1 ENSG00000141510       ENST00000269305
> >     5                       20
> >     2 ENSG00000133703       ENST00000256078
> >     1                        1
> >     3 ENSG00000133703       ENST00000311936
> >     1                        1
> >
> >
> >     Unfortunately you won't be able to get the affy id in the output
> >     but you
> >     can use biomaRt to map the Ensembl ids in the output back to the
> >     afffy ids.
> >
> >     Cheers,
> >     Steffen
> >
> >
> >     marco zucchelli wrote:
> >     > Hi,
> >     >
> >     >  I was wondering if it exists an annotation package for Affy
> >     133plus2
> >     > reporting the number of synonymous & non synonymous changes for
> the
> >     > genes on the array.
> >     >
> >     > If it does not exist does anybody has a good suggestion  about
> >     how to
> >     > retrive this information from databases ?
> >     >
> >     >
> >     > Marco
> >     >
> >     > _______________________________________________
> >     > Bioconductor mailing list
> >     > Bioconductor@stat.math.ethz.ch
> >     <mailto:Bioconductor@stat.math.ethz.ch>
> >     > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >     <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
>

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