[BioC] biomaRt Error : Affy Human Exon array annotation

Rashid, Mamunur mamunur.rashid at kcl.ac.uk
Tue Jul 6 14:11:39 CEST 2010


Dear List,

I have been trying to annotate some Affymetrix Human Exon Array Data 
using biomaRt. During the summarization I have played around with two
cdf Files. 

1. HuEx-1_0-st-v2,coreR3,A20071112,EP.CDF (Created by Elizabeth Purdom, UC Berkeley, created - 2007-11-12) 
    unitNames =  Affymetrix Transcript cluster IDs

   unitName groupName unit group cell
1   2315251   2315252    1     1    1
2   2315373   2315374    2     1    3
3   2315554   2315586    3     1    7
........

Q1. Is there any way to convert this affymetrix transcript cluster Ids ( 2315251 ) to gene symbol, or gene Names
       using biomaRt.?? If No then what could be the possible way to do it. ??

and 

2. HuEx-1_0-st-v2,U-Ensembl49,G-Affy.cdf  ( Mark Robinson, Elizabeth Purdom , updated - 2008-04-01 )
    unitNames = Ensembl Gene IDs

        unitName             groupName unit group cell
1  ENSG00000000003   4015402    1     1        1
2  ENSG00000000005   3984446    2     1      14
........

> ensembl = useMart("ensembl")
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
> filters = listFilters(ensembl)
> attributes = listAttributes(ensembl)

r1_2 <- getBM(attributes=c("strand","transcript_start","chromosome_name"),filters=c("ens_hs_gene"),values=c("ENSG00000000003"), mart= ensembl) 
            
I got the following error..

Error in getBM(attributes = c("strand", "transcript_start", "chromosome_name"),  : 
  Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_58.ox_Ens_Hs_gene__dm' doesn't exist

can any body please suggest what could be the possible reason for this.???
Any suggestion is welcome...

Thanks in advance

regards,
Mamun

R version 2.11.1 (2010-05-31) 
x86_64-unknown-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.4.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-2 XML_3.1-0  



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