[BioC] Agilent IDs and biomaRt package

[Cei Abreu-Goodger]

Hi Gonzalo,

R is trying to find the object called 'agilentprobe' (etc), all you need 
is to put it in quotes:

Agilent<-getGene(AgiIDs, type = "agilentprobe", mart=ensembl)

all your other arguments are actually ojects except that one...

Cheers,

Cei

On Fri, 11 Apr 2008, Gonzalo Gómez wrote:

> Hi all! I am trying to make a simple query for Agilent IDs in ensembl
> using biomaRt package. The code seems to be simple and vignettes are
> clear, however it fails...Im not sure if this could be a bug in biomaRt
> or in my code
>
> #My code is :
>
> >library(biomaRt)
> >ensembl = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
> >AgiIDs<-c("A_51_P227502" "A_52_P330395" "A_51_P183051")
>
> #I´ve tried:
>
> >Agilent<-getGene(AgiIDs, type = agilentprobe, mart=ensembl)
> Error in inherits(x, "factor") : object "agilentprobe" not found
>
> #and:
>
> >getBM(attributes = c("chromosome_name", "start_position"),
> filters=agilent-probe-2, values = AgiIDs, mart = ensembl)
> Error in inherits(x, "factor") : object "agilent" not found
>
> I´ve used listFilters(ensembl) in order to find the correct filters and
> type parametres and I also have used: agilent_probe but it doesn´t work
> anymore...
>
> >Agilent<-getGene(AgiIDs, type = agilent_probe, mart=ensembl)
> Error in inherits(x, "factor") : object "agilent_probe" not found
> >getBM(attributes = c("chromosome_name", "start_position"),
> filters=agilent_probe, values = AgiIDs, mart = ensembl)
> Error in inherits(x, "factor") : object "agilent_probe" not found
>
>
> Please, I´ll be very thankful if anybody can help me with this...
>
>
> Thanks
>
> Gonzalo
>
>
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