[BioC] biomRt package to get the 3'utr sequences of refseq predicted genes

[Harpreet Saini]

Hi,

I am getting some problem in using 'BiomaRt' package to obtain the 3'  
UTR sequences of refseq predicted genes. I am using the following  
command:
 > 
getSequence 
(id=refseqID,type="refseq_dna_predicted",seqType="3utr",mart=ensembl),  
where refseqId is a list of my refseq predicted genes.

I am getting the following error:

Error in getBM(c(seqType, type), filters = type, values = id, mart =  
mart,  :
   Invalid attribute(s): refseq_dna_predicted

I checked the filters and attributes also to confirm if the type is  
alright. It seems that the type should be 'refseq_dna_predicted'.

Any help would be great.

sessionInfo()
 > sessionInfo()
R version 2.7.2 (2008-08-25)
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] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GEOquery_2.4.5 Biobase_2.0.1  limma_2.14.6   biomaRt_1.14.1  
RCurl_0.9-4

loaded via a namespace (and not attached):
[1] XML_1.96-0


Thanks
Harpreet
Harpreet Kaur Saini
Enright Group
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge
CB10 1SD
Tel: +44-(0) 1223-492676