[BioC] Problem with biomaRt and retrieving annotation for the chip "affy_huex_1_0_st_v2"

[James W. MacDonald]

Hi Nenad,



Nenad Bartonicek wrote:
> Hello,
> 
> There seems to be a problem in retrieving annotation from the chip  
> "affy_huex_1_0_st_v2".
> 
>  >library(biomaRt)
>  >ensembl=useMart("ensembl",dataset="hsapiens_gene_ensembl")
> 
> Checking attributes and filters ... ok
> 
> #check if "affy_huex_1_0_st_v2" is a valid attribute
>  >attributes=listAttributes(ensembl)
>  >grep("affy_huex_1_0_st_v2",attributes[,1])
> 
> [1] 13
> 
> #collect data
>  >data=getBM(attributes="affy_huex_1_0_st_v2", mart=ensembl)

You are not asking for any data here. Do you get the same result if you 
include some values for the filter and values arguments?

Best,

Jim


> 
> Error in postForm(paste(martHost(mart), "?", sep = ""), query =  
> xmlQuery) :
>    transfer closed with outstanding read data remaining
> 
>  > sessionInfo()
> R version 2.8.1 (2008-12-22)
> i386-apple-darwin8.11.1
> 
> locale:
> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices datasets  tools     utils     methods
> [8] base
> 
> other attached packages:
> [1] biomaRt_1.16.0    R.utils_1.1.1     R.oo_1.4.6         
> R.methodsS3_1.0.3
> [5] Biobase_2.2.2
> 
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 XML_2.3-0
> 
> Thank you for your help,
> 
> Nenad
> 
> Nenad Bartonicek
> European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge
> CB10 1SD
> United Kingdom
> tel: +44-755-435-9057
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826