Entering edit mode
Paolo Innocenti
▴
320
@paolo-innocenti-2191
Last seen 10.2 years ago
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_IDEN
TIFICATION=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
>>
