[BioC] AffyID in biomaRt?

[Paolo Innocenti]

Hi all,

I am trying to get some information on genes (let's say Entrez IDs) 
through biomaRt, starting from my AffyIDs.
I am using drosophila2 Affymetrix chip.
Here's some code:

library(biomaRt)
mart <- useMart(biomart="ensembl",
	dataset="dmelanogaster_gene_ensembl")
grep("affy",c(listAttributes(mart),listFilters(mart)))
grep("drosophila2",c(listAttributes(mart),listFilters(mart)))
listAttributes(mart)[1:20,]
listFilters(mart)[1:20,]

and the output I got is attached.
My question is: how can I use biomaRt if there are no affy ID in either 
Attributes and Filters? Am I looking in the wrong place? I remember 
using it months ago, and it was working properly...

Best,
Paolo

>> library(biomaRt)
>> mart <- useMart(biomart="ensembl",
> + dataset="dmelanogaster_gene_ensembl")
> 
> Checking attributes and filters ... ok
>> grep("affy",c(listAttributes(mart),listFilters(mart)))
> integer(0)
>> grep("drosophila2",c(listAttributes(mart),listFilters(mart)))
> integer(0)
>> listAttributes(mart)[1:20,]
>                      name                 description
> 1        bdgp_insitu_expr            Bdgp insitu expr
> 2                 biotype                     Biotype
> 3         chromosome_name             Chromosome Name
> 4                    dedb                        Dedb
> 5             description                 Description
> 6                    embl           EMBL (Genbank) ID
> 7            end_position               Gene End (bp)
> 8     ensembl_cDNA_length         Ensembl cDNA length
> 9      ensembl_CDS_length          Ensembl CDS length
> 10        ensembl_gene_id             Ensembl Gene ID
> 11     ensembl_peptide_id          Ensembl Peptide ID
> 12 ensembl_peptide_length      Ensembl Peptide length
> 13  ensembl_transcript_id       Ensembl Transcript ID
> 14             entrezgene               EntrezGene ID
> 15          evidence_code            GO evidence code
> 16       external_gene_db                     Gene DB
> 17       external_gene_id                   Gene name
> 18                 family           Ensembl Family ID
> 19     family_description          Family Description
> 20           feat_chr_end Feature chromosome end (bp)
>> listFilters(mart)[1:20,]
>                            name            description
> 1                      band_end                   <NA>
> 2                    band_start                   <NA>
> 3              bdgp_insitu_expr Bdgp insitu expr ID(s)
> 4            bdgp_insitu_expr-2 Bdgp insitu expr ID(s)
> 5                  biol_process                   <NA>
> 6    biol_process_evidence_code                   <NA>
> 7                       biotype                   Type
> 8                cell_component                   <NA>
> 9  cell_component_evidence_code                   <NA>
> 10           chromosomal_region     Chromosome Regions
> 11              chromosome_name        Chromosome name
> 12                         dedb             Dedb ID(s)
> 13                       dedb-2             Dedb ID(s)
> 14                         embl             EMBL ID(s)
> 15                       embl-2             EMBL ID(s)
> 16                          end          Gene End (bp)
> 17               ensembl_family   Ensembl Family ID(s)
> 18              ensembl_gene_id     Ensembl Gene ID(s)
> 19            ensembl_gene_id-2     Ensembl Gene ID(s)
> 20           ensembl_peptide_id  Ensembl Peptide ID(s)
>> 
>> sessionInfo()
> R version 2.7.0 (2008-04-22) 
> i686-pc-linux-gnu 
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
>  [1] grid      splines   tools     stats     graphics  grDevices utils    
>  [8] datasets  methods   base     
> 
> other attached packages:
>  [1] pvclust_1.2-0        drosophila2cdf_2.2.0 Rgraphviz_1.18.0    
>  [4] drosophila2.db_2.2.0 affycoretools_1.12.0 annaffy_1.12.0      
>  [7] KEGG.db_2.2.0        biomaRt_1.14.0       RCurl_0.8-3         
> [10] GOstats_2.6.0        Category_2.6.0       RBGL_1.16.0         
> [13] GO.db_2.2.0          graph_1.18.0         limma_2.14.0        
> [16] hopach_1.14.0        cluster_1.11.10      affyQCReport_1.18.0 
> [19] geneplotter_1.18.0   annotate_1.18.0      AnnotationDbi_1.2.0 
> [22] RSQLite_0.6-8        DBI_0.2-4            lattice_0.17-6      
> [25] RColorBrewer_1.0-2   xtable_1.5-2         simpleaffy_2.16.0   
> [28] genefilter_1.20.0    survival_2.34-1      affyPLM_1.16.0      
> [31] gcrma_2.12.0         matchprobes_1.12.0   affy_1.18.0         
> [34] preprocessCore_1.2.0 affyio_1.8.0         Biobase_2.0.0       
> 
> loaded via a namespace (and not attached):
> [1] KernSmooth_2.22-22 XML_1.93-2        
>>