[BioC] biomaRt Error : Affy Human Exon array annotation

James W. MacDonald jmacdon at med.umich.edu
Tue Jul 6 15:49:25 CEST 2010


Hi Mamun,

On 7/6/2010 8:11 AM, Rashid, Mamunur wrote:
> 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. ??


 > getBM(attributes=c("strand","transcript_start","chromosome_name", 
"hgnc_symbol"),filters=c("affy_huex_1_0_st_v2"),values=c("2315252"),mart)
   strand transcript_start chromosome_name hgnc_symbol
1     -1           116086               8
2     -1            86649              11      OR4F2P
3      1        180794269               5       OR4F3
4      1        180794269               5      OR4F21
5      1           367640               1      OR4F29
6     -1           621096               1      OR4F16
7     -1           105919               6
8      1        170948694               6

This of course assumes that the groupName above is actually the probeset 
ID from the chip.

>
> 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

I think you want 'ensembl_gene_id' as a filter:

 > r1_2 <- 
getBM(attributes=c("strand","transcript_start","chromosome_name"),
filters=c("ensembl_gene_id"),values=c("ENSG00000000003"), mart)
 > r1_2
   strand transcript_start chromosome_name
1     -1         99883667               X
2     -1         99887538               X
3     -1         99888439               X
4     -1         99884691               X

Best,

Jim



>
> 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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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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