[ensembl-dev] Probe Mapping Problem

Ian Dunham dunham at ebi.ac.uk
Thu May 17 09:01:25 BST 2012


This will get you the list of all arrays

use Bio::EnsEMBL::Registry;
my $registry = "Bio::EnsEMBL::Registry";

$registry->load_registry_from_db(
     -host => 'ensembldb.ensembl.org', # alternatively 
'useastdb.ensembl.org'
     -user => 'anonymous'
);

my $aa = $registry->get_adaptor('mus musculus', 'funcgen', 'Array');

my @arrays = @{$aa->fetch_all()};
foreach my $array (@arrays){
	print "Name: " . $array->name() . "\nFormat: " . $array->format() 
."\nVendor: " . $array->vendor() . "\nType: ". $array->type() . 
"\nClass: ". $array->class() . "\n\n";
}


I'm pretty sure the one you want is

Name: MoGene-1_0-st-v1
Format: EXPRESSION
Vendor: AFFY
Type: OLIGO
Class: AFFY_ST


On 17/05/2012 02:45, JiangMei wrote:
> Hi.
>
> I'm trying to analyze the data generated by Affymetrix Mouse Gene 1.0 ST
> expression arrays. I tried to use Ensembl API to map their probe.
> However, I need to
> define the parameter fetch_by_name_vendor or fetch_by_name_class. I
> don't know the name API stores for the above platform.
>
> My perl script is attached below.
> =================================
> use Bio::EnsEMBL::Registry;
> use Bio::EnsEMBL::Funcgen::Array;
> my $registry = 'Bio::EnsEMBL::Registry';
> $registry->load_registry_from_db(
> -host =>'ensembldb.ensembl.org',
> -user =>'anonymous',
> -species =>'mus musculus',
> -db_version =>'65',
> );
> my $aa=$registry->get_adaptor('mus musculus','funcgen','array');
> my $array=$aa->fetc h_by_name_vendor('???', 'AFFY');
> my @probesets = @{$array->get_all_ProbeSets()};
> ==================================
> ??? denotes the platform name I need to input. How could I get it?
>
> Wish your help! Thanks very much!
>
> Best, Mei
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/




More information about the Dev mailing list