Hi Steffen et al,

Quick question about a search query via biomaRt. Here is the code that I am
using:

*****
library(biomaRt)
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
filters = listFilters(ensembl)
attributes = listAttributes(ensembl)
getBM(attributes=c("ensembl_peptide_id", "entrezgene",
               "ensembl_gene_id", "hgnc_automatic_gene_name"),
               filters="hgnc_automatic_gene_name", values="ATF4",
               mart=ensembl)
*****

For me, this returns an empty data frame. But when I query ATF4 online at
ensembl, I find what I need. I also looked up ATF4 at genenames.org (HUGO)
and it seems that ATF4 is a valid hgnc gene name, so the filter so be fine.
I guess the only other reason that I can see is which dataset I use in the
useMart function. I am guessing that the online API will search through all
datasets while I am only specifying a single one? If this is true, do you
know of a sensible work around? I have about 150 genes that I would like
mapped to the EBML ID names but using the code above with a vector of gene
names, I can only map around 25...but if I manually query for some of the
non-mapped gene names, I get what I am after. If I am wrong about my guess
in the dataset, can you let me know what you think might be going on?

Tony

> sessionInfo()
R version 2.11.0 Under development (unstable) (2010-01-16 r50993)
i386-apple-darwin10.2.0

locale:
[1] 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
[8] base

other attached packages:
 [1] hgu133plus2.db_2.3.5 org.Hs.eg.db_2.3.6   Rgraphviz_1.25.1
 [4] biomaRt_2.3.0        GOstats_2.13.0       RSQLite_0.8-1
 [7] DBI_0.2-5            Category_2.13.0      AnnotationDbi_1.9.4
[10] Biobase_2.7.3        RBGL_1.23.0          graph_1.25.5

loaded via a namespace (and not attached):
 [1] annotate_1.25.1   genefilter_1.29.5 GO.db_2.3.5       GSEABase_1.9.0
 [5] RCurl_1.3-1       splines_2.11.0    survival_2.35-8   tools_2.11.0
 [9] XML_2.6-0         xtable_1.5-6

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