biomaRt
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Fraser Sim ▴ 270
@fraser-sim-3567
Last seen 10.2 years ago
I'm having a problem with biomaRt today. Is the service down? Or do I have another problem? Thanks. > Hs.ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") Checking attributes ...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. > sessionInfo() R version 2.10.1 (2009-12-14) 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] grid stats graphics grDevices datasets utils methods [8] base other attached packages: [1] biomaRt_2.2.0 annotationTools_1.18.0 Biobase_2.6.1 [4] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1 [7] gdata_2.6.1 gtools_2.6.1 RColorBrewer_1.0-2 [10] RODBC_1.3-1 rcom_2.2-1 rscproxy_1.3-1 loaded via a namespace (and not attached): [1] RCurl_1.3-0 XML_2.6-0 Thanks, Fraser
biomaRt biomaRt • 2.2k views
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@james-w-macdonald-5106
Last seen 2 days ago
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Hi Fraser, On 7/13/2010 12:16 PM, Fraser Sim wrote: > I'm having a problem with biomaRt today. Is the service down? Or do I have > another problem? Thanks. Rather than asking here, wouldn't it be easier to just fire up a browser and see if the web service is available? That's what I just did, and I get no response, so there is your answer... Best, Jim > >> Hs.ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") > Checking attributes ...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. > >> sessionInfo() > R version 2.10.1 (2009-12-14) > 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] grid stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] biomaRt_2.2.0 annotationTools_1.18.0 Biobase_2.6.1 > [4] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1 > [7] gdata_2.6.1 gtools_2.6.1 RColorBrewer_1.0-2 > [10] RODBC_1.3-1 rcom_2.2-1 rscproxy_1.3-1 > > loaded via a namespace (and not attached): > [1] RCurl_1.3-0 XML_2.6-0 > > Thanks, > Fraser > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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@james-w-macdonald-5106
Last seen 2 days ago
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No, I am not talking about your internet connection, I am talking about the biomart web server at http://www.biomart.org/. The biomaRt package by default uses this web server, so if you cannot get the page to load in a browser, you will not be able to query using biomaRt either. Best, Jim On 7/13/2010 12:43 PM, Fraser Sim wrote: > My internet connection was fine if that's what you mean. I don't know how > else to check bioMart directly? Is there a link which shows the status of > the server? > > Cheers, > Fraser > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James W. > MacDonald > Sent: Tuesday, July 13, 2010 12:25 PM > To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] biomaRt > > Hi Fraser, > > On 7/13/2010 12:16 PM, Fraser Sim wrote: >> I'm having a problem with biomaRt today. Is the service down? Or do I have >> another problem? Thanks. > > Rather than asking here, wouldn't it be easier to just fire up a browser > and see if the web service is available? That's what I just did, and I > get no response, so there is your answer... > > > Best, > > Jim > > >> >>> Hs.ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl") >> Checking attributes ...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. >> >>> sessionInfo() >> R version 2.10.1 (2009-12-14) >> 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] grid stats graphics grDevices datasets utils methods >> [8] base >> >> other attached packages: >> [1] biomaRt_2.2.0 annotationTools_1.18.0 Biobase_2.6.1 >> [4] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1 >> [7] gdata_2.6.1 gtools_2.6.1 RColorBrewer_1.0-2 >> [10] RODBC_1.3-1 rcom_2.2-1 rscproxy_1.3-1 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.3-0 XML_2.6-0 >> >> Thanks, >> Fraser >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Hi Fraser, On Tue, Jul 13, 2010 at 1:19 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > No, I am not talking about your internet connection, I am talking about the > biomart web server at http://www.biomart.org/. The biomaRt package by > default uses this web server, so if you cannot get the page to load in a > browser, you will not be able to query using biomaRt either. I think some people get confused and think the biomart service is something owned/operated by the bioconductor folks: it's not. As Jim points out, the web server is here: http://biomart.org The bioconductor package "biomaRt" is simply an R library that calls out to the biomart.org service with well-formed URL's that are built by the criteria constructed in your getBM (or whatever) function calls. If biomart.org is down, then your getBM calls will also fail, but there's nothing that can be done about that on this list. Probably your best bet is to contact the biomart.org people directly. That having been said, it seems that biomart.org is back up now. Hope that clears things up (if they needed clearing to begin with :-). -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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And to expand on this a bit further, you don't have to use the default biomart server. For instance, if biomart.org is down, you could presumably use the biomart server that Ensembl has set up. As I am in the US, my local ensembl server is uswest.ensembl.org, so > listMarts(host="uswest.ensembl.org", path="/biomart/martservice") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 58 2 ENSEMBL_MART_SNP Ensembl Variation 58 3 ENSEMBL_MART_FUNCGEN Ensembl Functional Genomics 58 4 ENSEMBL_MART_VEGA Vega 38 5 REACTOME Reactome 6 wormbase195 WormBase 195 (CSHL US) 7 pride PRIDE (EBI UK) > mart <- useMart("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl", host="uswest.ensembl.org", path="/biomart/martservice") Checking attributes ... ok Checking filters ... ok> Note that the ensembl server is a bit more schizophrenic than the biomart server, so if you get an error like this, then you may need to try again: > mart <- useMart("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl", host="uswest.ensembl.org", path="/biomart/martservice") Checking attributes ...Error in bmAttrFilt("attributes", mart) : biomaRt error: looks like we're connecting to incompatible version of BioMart suite. I got this error directly after a successful connection, so there you go. > getBM(c("affy_hg_u133_plus_2", "entrezgene"), "affy_hg_u133_plus_2", "1007_s_at",mart) affy_hg_u133_plus_2 entrezgene 1 1007_s_at 780 2 1007_s_at NA Best, Jim On 7/13/2010 2:17 PM, Steve Lianoglou wrote: > Hi Fraser, > > On Tue, Jul 13, 2010 at 1:19 PM, James W. MacDonald > <jmacdon at="" med.umich.edu=""> wrote: >> No, I am not talking about your internet connection, I am talking about the >> biomart web server at http://www.biomart.org/. The biomaRt package by >> default uses this web server, so if you cannot get the page to load in a >> browser, you will not be able to query using biomaRt either. > > I think some people get confused and think the biomart service is > something owned/operated by the bioconductor folks: it's not. > > As Jim points out, the web server is here: > http://biomart.org > > The bioconductor package "biomaRt" is simply an R library that calls > out to the biomart.org service with well-formed URL's that are built > by the criteria constructed in your getBM (or whatever) function > calls. > > If biomart.org is down, then your getBM calls will also fail, but > there's nothing that can be done about that on this list. Probably > your best bet is to contact the biomart.org people directly. > > That having been said, it seems that biomart.org is back up now. > > Hope that clears things up (if they needed clearing to begin with :-). > -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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