[BioC] BiomaRt query

Wolfgang Huber whuber at embl.de
Tue Mar 23 09:25:12 CET 2010


have you checked the sequence of the probe A_51_P227502 and aligned 
(e.g. 'blasted') it against the genome? One possible explanation for 
what you see is that (with current genome build and annotation) Ensembl 
might no longer link this probe to a mouse gene.

	Best wishes

De Boever Patrick ha scritto:
> Hi all,
> I did a biomaRt query with the most recent package and R2.10.
> Although my query involves 3 Agilent (mouse) probes, I get results for 2 probes. This is consistent, also with other probes?
> The code is pasted below.
> Can anybody give support on this trivial question.
> Thank you,
> Patrick
>> AgiIDs<- c("A_51_P227502","A_52_P330395","A_51_P183051")
>> Agilent<-getGene(AgiIDs, type = 'agilent_wholegenome', mart=ensembl)
>> Agilent
>   agilent_wholegenome mgi_symbol                                                                                                          description
> 1        A_51_P183051       Upb1                                                      ureidopropionase, beta Gene [Source:MGI Symbol;Acc:MGI:2143535]
> 2        A_52_P330395      Farp1 FERM, RhoGEF (Arhgef) and pleckstrin domain protein 1 (chondrocyte-derived) Gene [Source:MGI Symbol;Acc:MGI:2446173]
>   chromosome_name band strand start_position end_position    ensembl_gene_id
> 1              10   C1      1       74869656     74904424 ENSMUSG00000033427
> 2              14   E5      1      121434422    121682966 ENSMUSG00000025555
> Patrick De Boever, PhD, MSc
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Best wishes

Wolfgang Huber

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