Hi,
I have been trying to work with an archived version of ensembl mart, i.e.
ensembl_46. The code goes as follow:

>library(biomaRt)
>#listMarts(archive=TRUE)
>mart=useMart("ensembl_mart_46", archive=TRUE)
>## listDatasets(mart)
>mart=useDataset("mmusculus_gene_ensembl",mart)
Checking attributes ... ok
Checking filters ... ok
Warning messages:
1: In bmAttrFilt("attributes", mart) :
  biomaRt warning: looks like we're connecting to an older version of
BioMart suite. Some biomaRt functions might not work.
2: In bmAttrFilt("filters", mart) :
  biomaRt warning: looks like we're connecting to an older version of
BioMart suite. Some biomaRt functions might not work.

> plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, end =
30550000, strand = "+", biomart = mart)


I have modified the GeneRegion method such that it can work with older,
hardcoded attribute names. It started to give error once again due to
"strand" not being one of the filters supported by old ensembl build.
Therefore, I tried a simpler way to collect genomic features from biomart  :

 > getBM(c("gene_stable_id","transcript_stable_id",

"exon_stable_id","exon_chrom_start","exon_chrom_end",
                                "rank",
"transcript_chrom_strand","struct_biotype"),

filters=c("chromosome_name","start","end"),values=list(17,30450000,30455000),mart)

Error in listFilters(mart, what = "type") :
The function argument 'what' contains an invalid value: type
Valid are: name, description, options, fullDescription

I also tried out with listFilters function :
listFilters("chromosome_name",mart=mart), which results in the same error.

What is going on here, and how can I rectify it ?

Here is my session info:

R version 2.9.1 (2009-06-26)
i386-apple-darwin8.11.1

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] GenomeGraphs_1.0.1 biomaRt_2.0.0

loaded via a namespace (and not attached):
[1] RCurl_0.94-1 XML_2.6-0


Thanks,
Tejal

	[[alternative HTML version deleted]]

