[BioC] biomRt package to get the 3'utr sequences of refseq predicted genes
Harpreet Saini
hsaini at ebi.ac.uk
Tue Oct 28 11:54:44 CET 2008
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
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