[BioC] Biomart with human genes NCBI 35

[James W. MacDonald]

Hi Marco,

marco zucchelli wrote:
> Dear James and Steffen,
> 
> thanks , workks properly now. At the same time seems that the functions
> defined in biomaRt do not work on
> the archived versions.

Actually, your code doesn't work with the MySQL interface regardless of 
the dataset. Although, interestingly enough the error message is 
different depending on what dataset you use.

 > mart <- useMart("ensembl","hsapiens_gene_ensembl", mysql=T)
Loading required package: RMySQL
Loading required package: DBI
connected to:  ensembl
Reading database configuration of: hsapiens_gene_ensembl
Checking attributes and filters ... ok
Checking main tables ... ok

 > gene.list <- getFeature(chromosome=1, type="entrezgene", mart=mart)
Error in queryGenerator(attributes = attributes, filter = filters, 
values = values,  :
	'length(filter)' must be 1 when using biomaRt in MySQL mode.
 > ensmart <- useMart("ensembl_mart_37",dataset="hsapiens_gene_ensembl",
mysql=TRUE,archive=TRUE)
connected to:  ensembl_mart_37
Reading database configuration of: hsapiens_gene_ensembl
Checking attributes and filters ... ok
Checking main tables ... ok
 > gene.list <- getFeature(chromosome=1, type="entrezgene", mart=ensmart)
Error in getFeature(chromosome = 1, type = "entrezgene", mart = ensmart) :
	This function only works when using to ensembl. To use this function 
use: mart =  useMart('ensembl')

## This works

 > cmart <- useMart("ensembl", "hsapiens_gene_ensembl")
Checking attributes and filters ... ok
 > gene.list <- getFeature(chromosome=1, type="entrezgene", mart=cmart)
 > gene.list
      chromosome_name entrezgene
1                  1      79501
2                  1      26683
3                  1      81399
4                  1     729759

This looks like something for Steffen.

Best,

Jim

> 
> #######
>> ensmart       <-
> useMart("ensembl_mart_37",dataset="hsapiens_gene_ensembl",mysql=TRUE,archive=TRUE) 
> 
> connected to:  ensembl_mart_37
> Reading database configuration of: hsapiens_gene_ensembl
> Checking attributes and filters ... ok
> Checking main tables ... ok
>>  gene.list           <- getFeature(chromosome=1,type="entrezgene",
> mart=ensmart)
> Error in getFeature(chromosome = 1, type = "entrezgene", mart = ensmart) :
>    This function only works when using to ensembl. To use this function
> use: mart =  useMart('ensembl')
> ########


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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