[BioC] Agilent IDs and biomaRt package

[Sean Davis]

On Fri, Apr 11, 2008 at 11:06 AM, Gonzalo Gómez <ggomez at cnio.es> 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...

Hi, Gonzalo.  Your AgiIDs needs some commas.  I think you need some
extra quotes around agilent_probe and agilent?  Does that help?  If
not, do not forget to include sessionInfo() if you need more help.

Sean