[BioC] error with biomaRt in mysql mode

[Janet Young]

Hi James,

Thanks - that was very helpful.

(For my chr_name filter, I'll use values=c(1:22,"X","Y"), rather than  
1:24)

Janet

On Dec 23, 2007, at 11:23 AM, James MacDonald wrote:

> Hi Janet,
>
> Janet Young wrote:
>> Hi,
>> I'm having trouble using biomaRt in mysql mode to access genes  
>> from  an older human assembly (NCBI35).
>> My query works fine in the web query mode:
>>  > ensemblnew<-useMart("ensembl",dataset="hsapiens_gene_ensembl")
>> Checking attributes and filters ... ok
>>  > allgenes<-getBM( c("hgnc_symbol","go","entrezgene"),  
>> mart=ensemblnew)
>>  > dim(allgenes)
>> [1] 184982      3
>> but now I'm trying to work with the older assembly, and get the   
>> following error with getBM:
>>  > ensemblmysql<-useMart  
>> ("ensembl_mart_37",dataset="hsapiens_gene_ensembl",archive=T,mysql=T)
>> connected to:  ensembl_mart_37
>> Reading database configuration of: hsapiens_gene_ensembl
>> Checking attributes and filters ... ok
>> Checking main tables ... ok
>>  > allgenesmysql<-getBM( c("hgnc_symbol","go_id","entrezgene"),   
>> mart=ensemblmysql)
>> Error in exists(filter, martFilters(mart)) : invalid first argument
>
> You need to specify a filter and value. Might be a better way to do  
> this but:
>
> > mart <- useMart("ensembl_mart_37", "hsapiens_gene_ensembl",  
> archive=T, mysql=T)
> connected to:  ensembl_mart_37
> Reading database configuration of: hsapiens_gene_ensembl
> Checking attributes and filters ... ok
> Checking main tables ... ok
> > tmp2 <- getBM(c("hgnc_symbol", "go_id",  
> "entrezgene"),filters="chr_name", values=c(1:24), mart=mart)
> > dim(tmp2)
> [1] 177700      3
>
> Lots of <NA> in that table -- you might be better off using  
> output="list", but that's up to you.
>
> Best,
>
> Jim
>
>
>> I also tried it with ensembl_mart_47, substituting "go" for  
>> "go_id"  and it gave the same error.   I can't figure out whether  
>> I've found a  bug, or I'm just doing something wrong.
>> My sessionInfo output is below. I noticed that my RMySQL_0.6-0 is   
>> loaded in my session, but not the sessionInfo output given in the   
>> vignette (might be using RSQLite_0.6-4 instead) - could that be   
>> something to do with it?
>>  > sessionInfo()
>> R version 2.6.1 (2007-11-26)
>> i386-apple-darwin8.10.1
>> locale:
>> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> other attached packages:
>> [1] RMySQL_0.6-0   DBI_0.2-4      biomaRt_1.12.2 RCurl_0.8-3
>> loaded via a namespace (and not attached):
>> [1] XML_1.93-2
>> thanks in advance for any help,
>> Janet Young
>> -------------------------------------------------------------------
>> Dr. Janet Young (Trask lab)
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Avenue N., C3-168,
>> P.O. Box 19024, Seattle, WA 98109-1024, USA.
>> tel: (206) 667 1471 fax: (206) 667 6524
>> email: jayoung at fhcrc.org
>> http://www.fhcrc.org/labs/trask/
>> _______________________________________________
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>
> -- 
> James W. MacDonald, MS
> Biostatistician
> UMCCC cDNA and Affymetrix Core
> University of Michigan
> 1500 E Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623