[BioC] how to do it with biomaRt

[Alex Sanchez]

Hello Michal

> The trick is that your IDs in the biomaRt filter are neither transcripts 
> nor compatible with "affy_raex_1_0_st_v1".
It explains the empty return

> Your IDs are Affy transcript clusters - a bit old way of defining features 
> on the Affy Exon chips, abandoned as
> far as I know in most of the software, perhaps except GeneSpring 10 and 
> NetAffx.

It is also used by the "fastuos" Partek Genomics Suite.

> One transcript cluster consists of several probesets, eg your first 
> transcript cluster has 5 probesets (check with NetAffx).
> Then - those probeset IDs are compatible with your "affy_raex_1_0_st_v1" 
> filter and will give you results.

> Btw, the job of translating rat exon probesets into genes and transcripts 
> is done most quickly with exonmap,
> assuming that you install a local copy of X:MAP database...

The point is that, what we often do, is to use Gene Array or Exon chips to 
study gene expression -not alternative splicing- so what I am looking for is 
a flexible way to get the annotations for these chips a the transcript 
cluster level.

Thanks for the help

Alex


----- Original Message ----- 
From: "Michal Okoniewski" <michal.okoniewski at fgcz.ethz.ch>
To: "Alex Sanchez" <asanchez at ub.edu>; <bioconductor at stat.math.ethz.ch>
Cc: <jlmosquera at ir.vhebron.net>; "M. Carme Ruiz de Villa" 
<mruiz_de_villa at ub.edu>
Sent: Thursday, November 05, 2009 7:04 AM
Subject: RE: [BioC] how to do it with biomaRt


Hello Alex,

The trick is that your IDs in the biomaRt filter are neither transcripts nor 
compatible with "affy_raex_1_0_st_v1".

Your IDs are Affy transcript clusters - a bit old way of defining features 
on the Affy Exon chips, abandoned as
far as I know in most of the software, perhaps except GeneSpring 10 and 
NetAffx.

One transcript cluster consists of several probesets, eg your first 
transcript cluster has 5 probesets (check with NetAffx).
Then - those probeset IDs are compatible with your "affy_raex_1_0_st_v1" 
filter and will give you results.

Btw, the job of translating rat exon probesets into genes and transcripts is 
done most quickly with exonmap,
assuming that you install a local copy of X:MAP database...

Saludos!
Michal


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Alex Sanchez
Sent: Wed 11/4/2009 11:29 PM
To: bioconductor at stat.math.ethz.ch
Cc: jlmosquera at ir.vhebron.net; M. Carme Ruiz de Villa
Subject: [BioC] how to do it with biomaRt

Hello

I am trying to use biomaRt for what seems to be a simple query.

I have a list of transcript IDs from affymetrix Rat Exon arrays.
I would like to get some associated identifiers such as the entrez gene id 
or th gene symbol.

I have done the following

######################
library("biomaRt")

### Seleccio de la base de dades i el 'dataset' (aquest darrer ve definit 
per l'organisme)
ensemblMart<- useMart("ensembl")
# listDatasets (ensemblMart) # omitted in the message
ensemblMart <- useMart("ensembl", dataset="rnorvegicus_gene_ensembl")
# ratFilters<-listFilters(ensemblMart) # omitted in the message
filters1 <- "affy_raex_1_0_st_v1"
transcriptIDs1 <- c("7241279","7332324","7241281","7199205","7112511")
# listAttributes(ensemblMart)  # omitted in the message
attributes1 <-c("affy_raex_1_0_st_v1","entrezgene","rgd_symbol")
getBM(attributes = attributes1,
       filters=filters1,
       values=transcriptIDs1,
       mart=ensemblMart)
#######################
but I obtain an empty result

[1] affy_raex_1_0_st_v1 entrezgene          rgd_symbol
<0 rows> (or 0-length row.names)

#######################
I have used R 2.9 in Ubuntu and windows and I have obtained the same 
results.
I presume I must be doing something wrong because these IDs do have entrez 
gene and symbol IDs
(Verified in NetAffy)

Any help will be appreciated.

Thanks

Alex Sánchez
-----------------------------------------------------------------------------------------------------
Dr. Alex  Sánchez. Statistics Department. University of Barcelona.
Facultat de Biologia UB. Avda Diagonal 645. 08028 Barcelona. Spain
asanchez_at_ub.edu
Statistics and Bioinformatics Unit
Institut de Recerca. Hospital Universitari Vall 'Hebron
Passeig Vall d'Hebron 112-119. 08034 Barcelona
asanchez_at_ir.vhebron.net
----------------------------------------------------------------------------------------------------







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