[BioC] error with biomaRt in mysql mode

[Janet Young]

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

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/