(Sorry if you received this email twice)

Hi all,

I am currently experiencing problems running biomaRt package.
I have a simple task to do which consists in retrieving all hgnc symbols
between two genomic positions on a chromosome.

My genomic positions are mapped to NCBI36/hg18 so I want to use an archived
version of ensembl database to be able to query this human genome version.

I am behind a proxy. I am using a windows PC, pentium 4, 3.2 Ghz, 1 Go RAM.

I have already been through the archived mailing list to find useful
information about problems running biomaRt. And this allowed me to get
started and below you will find the scripts I used and my sessionInfo().


I can connect to the release 54 (NCBI36) of ensembl database, create a
'biomart object' but the getBM function fails. A traceback() call indicates
that the error comes from a call to tryCatch(..). The error is the following
:

*Erreur dans 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.
De plus : Message d'avis :
In getStatus(status) : NAs introduits lors de la conversion automatique*

But it seems that my internet connection is not down and neither is biomart
web service.

Does anyone know why I am getting this message ?
Any help would be appreciated. Thank you very much.


Anthony Ferrari




> Sys.time()
[1] "2010-03-24 09:57:42 CET"
> library(biomaRt);
> Sys.setenv("http_proxy"="http://195.220.67.254:8247");
>
> listMarts(host="may2009.archive.ensembl.org",path="/
biomart/martservice",archive=FALSE);
               biomart              version
1 ENSEMBL_MART_ENSEMBL           Ensembl 54
2     ENSEMBL_MART_SNP Ensembl Variation 54
3    ENSEMBL_MART_VEGA              Vega 35
4             REACTOME   Reactome(CSHL US)
5     wormbase_current   WormBase (CSHL US)
6                pride       PRIDE (EBI UK)
> ensembl =
useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host="
may2009.archive.ensembl.org",path="/biomart/martservice",archive=FALSE);
Checking attributes ... ok
Checking filters ... ok
>
> chrom <- 5;
> chr.start <- 110000000;
> chr.stop  <- 113000000;
>
>
getBM(attributes="hgnc_symbol",filters=c("chromosome_name","start","end"),values=list(chrom,chr.start,chr.stop),mart=ensembl);
Erreur dans 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.
De plus : Message d'avis :
In getStatus(status) : NAs introduits lors de la conversion automatique
>
> traceback()
6: stop("Request to BioMart web service failed. Verify if you are still
connected to the internet.  Alternatively the BioMart web service is
temporarily down.")
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch(postForm(paste(martHost(mart), "?", sep = ""), query =
xmlQuery),
       error = function(e) {
           stop("Request to BioMart web service failed. Verify if you are
still connected to the internet.  Alternatively the BioMart web service is
temporarily down.")
       })
1: getBM(attributes = "hgnc_symbol", filters = c("chromosome_name",
       "start", "end"), values = list(chrom, chr.start, chr.stop),
       mart = ensembl)
>
> Sys.time()
[1] "2010-03-24 09:57:47 CET"
>
> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252

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

other attached packages:
[1] biomaRt_2.2.0

loaded via a namespace (and not attached):
[1] RCurl_1.3-1 XML_2.8-1
>

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