[BioC] getBM no connection but listMarts has

[James W. MacDonald]

Hi Cristobal,

Cristobal Fresno Rodríguez wrote:
> Hi,
> 
> I'm trying to use biomaRt but get the following error, when I try getBM
> statement but the connectivity seems ok according to listMarts().
> 
> library("biomaRt")
> listMarts()[1:4,]
>               biomart
>              version
> 1             ensembl               ENSEMBL 56 GENES (SANGER UK)
> 2                 snp          ENSEMBL 56 VARIATION  (SANGER UK)
> 3 functional_genomics ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK)
> 4                vega                       VEGA 36  (SANGER UK)
> ensembl = useMart("ensembl")
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
> Checking attributes ... ok
> Checking filters ... ok
> affyids = c("202763_at", "209310_s_at", "207500_at")
> getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters =
> "affy_hg_u133_plus_2", values = affyids, mart = ensembl)
> Error in value[[3L]](cond) :
>   Request to BioMart web service failed. Verify if you are still connected
> to the internet.  Alternatively the BioMart web service is temporarily down.
> Calls: getBM ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
> 
> 
> I search a little bit and found that on the postForm call on getBM got the
> error; probably RCurl compatibility issue?

Possibly. You have a previous version of R and a current version of 
biomaRt and RCurl. This works for me with packages installed using 
biocLite():

 > library(biomaRt)
 > ensembl <- useMart("ensembl", "hsapiens_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
 > affyids = c("202763_at", "209310_s_at", "207500_at")
 >
 > getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters 
="affy_hg_u133_plus_2", values = affyids, mart = ensembl)
   affy_hg_u133_plus_2 entrezgene
1           202763_at        836
2           202763_at         NA
3         209310_s_at        837
4         209310_s_at         NA
5           207500_at        838
6           207500_at         NA
 > > > sessionInfo()
R version 2.10.0 Patched (2009-11-05 r50317)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] biomaRt_2.2.0

loaded via a namespace (and not attached):
[1] RCurl_1.2-1 XML_2.6-0

Best,

Jim
> 
> 
>> sessionInfo()
> R version 2.9.2 (2009-08-24)
> i486-pc-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHONE=en_US.UTF-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] biomaRt_2.2.0 rkward_0.5.1
> 
> loaded via a namespace (and not attached):
> [1] RCurl_1.3-0 tools_2.9.2 XML_2.6-0
> 
> 
> Thanks,
> 
> Cristobal
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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