[biomart-users] Error: Expectation Failed. Converting human refseq genes to mouse ensembl ENSMG

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[biomart-users] Error: Expectation Failed. Converting human refseq genes to mouse ensembl ENSMG

Darya Vanichkina
Hi! I'm having trouble once again running code that successfully worked last week (!). 

Briefly, I am trying to convert a list of human refseq mRNA gene identifiers to mouse ENSMG gene names. The commands and tracebacks I am using are the following:

library(biomaRt)
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", verbose = TRUE)

Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Mart host: http://www.ensembl.org:80/biomart/martservice
Checking attributes ...Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=attributes&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok
Checking filters ...Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=filters&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok

mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl", verbose = TRUE)
Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Mart host: http://www.ensembl.org:80/biomart/martservice
Checking attributes ...Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=attributes&dataset=mmusculus_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok
Checking filters ...Attempting web service request:
http://www.ensembl.org:80/biomart/martservice?type=filters&dataset=mmusculus_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok

mousegenes <-getLDS(attributes = c("ensembl_gene_id"), filters = "refseq_mrna", values = c("NM_016607","NM_022838","NM_001668"), mart = human, attributesL = c("ensembl_gene_id"), martL = mouse, verbose = TRUE)

<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= "biomaRt"> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Filter name = 'refseq_mrna' value = 'NM_016607,NM_022838,NM_001668' /></Dataset><Dataset name = 'mmusculus_gene_ensembl' ><Attribute name = 'ensembl_gene_id'/></Dataset></Query>
Error: Expectation Failed

traceback()

4: stop(err)
3: stop.if.HTTP.error(http.header)
2: postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery)
1: getLDS(attributes = c("ensembl_gene_id"), filters = "refseq_mrna", 
       values = c("NM_016607", "NM_022838", "NM_001668"), mart = human, 
       attributesL = c("ensembl_gene_id"), martL = mouse, verbose = TRUE)

sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] genefilter_1.52.1          plyr_1.8.3                 hwriter_1.3.2              gplots_2.17.0             
 [5] DESeq2_1.10.1              RcppArmadillo_0.6.500.4.0  Rcpp_0.12.3                SummarizedExperiment_1.0.2
 [9] Biobase_2.30.0             GenomicRanges_1.22.4       GenomeInfoDb_1.6.3         IRanges_2.4.8             
[13] S4Vectors_0.8.11           BiocGenerics_0.16.1        gridExtra_2.2.1            biomaRt_2.26.1            
[17] edgeR_3.12.0               limma_3.26.8               reshape2_1.4.1             RColorBrewer_1.1-2        
[21] data.table_1.9.6           ggplot2_2.1.0             

loaded via a namespace (and not attached):
 [1] gtools_3.5.0         locfit_1.5-9.1       splines_3.2.3        lattice_0.20-33      colorspace_1.2-6    
 [6] chron_2.3-47         XML_3.98-1.4         survival_2.38-3      foreign_0.8-66       DBI_0.3.1           
[11] BiocParallel_1.4.3   lambda.r_1.1.7       stringr_1.0.0        zlibbioc_1.16.0      munsell_0.4.3       
[16] gtable_0.2.0         futile.logger_1.4.1  caTools_1.17.1       labeling_0.3         latticeExtra_0.6-28 
[21] geneplotter_1.48.0   AnnotationDbi_1.32.3 KernSmooth_2.23-15   acepack_1.3-3.3      xtable_1.8-2        
[26] scales_0.4.0         gdata_2.17.0         Hmisc_3.17-2         annotate_1.48.0      XVector_0.10.0      
[31] digest_0.6.9         stringi_1.0-1        grid_3.2.3           tools_3.2.3          bitops_1.0-6        
[36] magrittr_1.5         RCurl_1.95-4.8       RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.3       
[41] futile.options_1.0.0 rpart_4.1-10         nnet_7.3-12   


Why has my command stopped working???

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Re: [biomart-users] Error: Expectation Failed. Converting human refseq genes to mouse ensembl ENSMG

Thomas Maurel
Dear Darya,

I’ve just tried your query and it’s working fine for me:

> library(biomaRt)
> mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl", verbose = TRUE)
Attempting web service request:
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Checking attributes ...Attempting web service request:
 ok
Checking filters ...Attempting web service request:
 ok
> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", verbose = TRUE)
Attempting web service request:
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Checking attributes ...Attempting web service request:
 ok
Checking filters ...Attempting web service request:
 ok
> mousegenes <-getLDS(attributes = c("ensembl_gene_id"), filters = "refseq_mrna", values = c("NM_016607","NM_022838","NM_001668"), mart = human, attributesL = c("ensembl_gene_id"), martL = mouse, verbose = TRUE)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= "biomaRt"> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Filter name = 'refseq_mrna' value = 'NM_016607,NM_022838,NM_001668' /></Dataset><Dataset name = 'mmusculus_gene_ensembl' ><Attribute name = 'ensembl_gene_id'/></Dataset></Query>
> mousegenes
  Ensembl.Gene.ID  Ensembl.Gene.ID.1
1 ENSG00000125962 ENSMUSG00000072969
2 ENSG00000102401 ENSMUSG00000049047
3 ENSG00000143437 ENSMUSG00000015522

Maybe it was an internet connection glitch or the server was really busy.
Hope this helps,
Best Regards,
Thomas
On 21 Mar 2016, at 07:18, Darya Vanichkina <[hidden email]> wrote:

Hi! I'm having trouble once again running code that successfully worked last week (!). 

Briefly, I am trying to convert a list of human refseq mRNA gene identifiers to mouse ENSMG gene names. The commands and tracebacks I am using are the following:

library(biomaRt)
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", verbose = TRUE)

Attempting web service request:
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Checking attributes ...Attempting web service request:
 ok
Checking filters ...Attempting web service request:
 ok

mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl", verbose = TRUE)
Attempting web service request:
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Checking attributes ...Attempting web service request:
 ok
Checking filters ...Attempting web service request:
 ok

mousegenes <-getLDS(attributes = c("ensembl_gene_id"), filters = "refseq_mrna", values = c("NM_016607","NM_022838","NM_001668"), mart = human, attributesL = c("ensembl_gene_id"), martL = mouse, verbose = TRUE)

<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= "biomaRt"> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Filter name = 'refseq_mrna' value = 'NM_016607,NM_022838,NM_001668' /></Dataset><Dataset name = 'mmusculus_gene_ensembl' ><Attribute name = 'ensembl_gene_id'/></Dataset></Query>
Error: Expectation Failed

traceback()

4: stop(err)
3: stop.if.HTTP.error(http.header)
2: postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery)
1: getLDS(attributes = c("ensembl_gene_id"), filters = "refseq_mrna", 
       values = c("NM_016607", "NM_022838", "NM_001668"), mart = human, 
       attributesL = c("ensembl_gene_id"), martL = mouse, verbose = TRUE)

sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] genefilter_1.52.1          plyr_1.8.3                 hwriter_1.3.2              gplots_2.17.0             
 [5] DESeq2_1.10.1              RcppArmadillo_0.6.500.4.0  Rcpp_0.12.3                SummarizedExperiment_1.0.2
 [9] Biobase_2.30.0             GenomicRanges_1.22.4       GenomeInfoDb_1.6.3         IRanges_2.4.8             
[13] S4Vectors_0.8.11           BiocGenerics_0.16.1        gridExtra_2.2.1            biomaRt_2.26.1            
[17] edgeR_3.12.0               limma_3.26.8               reshape2_1.4.1             RColorBrewer_1.1-2        
[21] data.table_1.9.6           ggplot2_2.1.0             

loaded via a namespace (and not attached):
 [1] gtools_3.5.0         locfit_1.5-9.1       splines_3.2.3        lattice_0.20-33      colorspace_1.2-6    
 [6] chron_2.3-47         XML_3.98-1.4         survival_2.38-3      foreign_0.8-66       DBI_0.3.1           
[11] BiocParallel_1.4.3   lambda.r_1.1.7       stringr_1.0.0        zlibbioc_1.16.0      munsell_0.4.3       
[16] gtable_0.2.0         futile.logger_1.4.1  caTools_1.17.1       labeling_0.3         latticeExtra_0.6-28 
[21] geneplotter_1.48.0   AnnotationDbi_1.32.3 KernSmooth_2.23-15   acepack_1.3-3.3      xtable_1.8-2        
[26] scales_0.4.0         gdata_2.17.0         Hmisc_3.17-2         annotate_1.48.0      XVector_0.10.0      
[31] digest_0.6.9         stringi_1.0-1        grid_3.2.3           tools_3.2.3          bitops_1.0-6        
[36] magrittr_1.5         RCurl_1.95-4.8       RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.3       
[41] futile.options_1.0.0 rpart_4.1-10         nnet_7.3-12   


Why has my command stopped working???

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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] Error: Expectation Failed. Converting human refseq genes to mouse ensembl ENSMG

Darya Vanichkina
Hi Thomas,

So by trying this at home/ at a cafe/ at work, I've been able to pinpoint that this - as well as a previous post of mine - must be the result of an institute firewall issue. 

I think that the problems described here and here are probably similar to mine?...

What ports, protocols and authentication types does biomaRt require to work properly? I know about 80, but it must be more than that, since port 80 is pretty heavily used, and I haven't had any other issues with it from work.

Thanks in advance,
Darya

On Tuesday, 22 March 2016 04:42:07 UTC+11, Thomas Maurel wrote:
Dear Darya,

I’ve just tried your query and it’s working fine for me:

> library(biomaRt)
> mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl", verbose = TRUE)
Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=version&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dversion%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL\46sa\75D\46sntz\0751\46usg\75AFQjCNGKpzSHsLMlFq5HOkWjmDhGz4UU5A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dversion%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL\46sa\75D\46sntz\0751\46usg\75AFQjCNGKpzSHsLMlFq5HOkWjmDhGz4UU5A&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Mart host: <a href="http://www.ensembl.org:80/biomart/martservice" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice\46sa\75D\46sntz\0751\46usg\75AFQjCNF84P8pBVtfNkFTkCUKHEj3h9pmqg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice\46sa\75D\46sntz\0751\46usg\75AFQjCNF84P8pBVtfNkFTkCUKHEj3h9pmqg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice
Checking attributes ...Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=attributes&amp;dataset=mmusculus_gene_ensembl&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL&amp;virtualSchema=default" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dattributes%26dataset%3Dmmusculus_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNHmIuwaUDVM82671RLYatoIl2q7Uw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dattributes%26dataset%3Dmmusculus_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNHmIuwaUDVM82671RLYatoIl2q7Uw&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=attributes&dataset=mmusculus_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok
Checking filters ...Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=filters&amp;dataset=mmusculus_gene_ensembl&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL&amp;virtualSchema=default" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dfilters%26dataset%3Dmmusculus_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNFjI79fs5Y6l1blVvTl1kSsWzeshg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dfilters%26dataset%3Dmmusculus_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNFjI79fs5Y6l1blVvTl1kSsWzeshg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=filters&dataset=mmusculus_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok
> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", verbose = TRUE)
Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=version&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dversion%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL\46sa\75D\46sntz\0751\46usg\75AFQjCNGKpzSHsLMlFq5HOkWjmDhGz4UU5A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dversion%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL\46sa\75D\46sntz\0751\46usg\75AFQjCNGKpzSHsLMlFq5HOkWjmDhGz4UU5A&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Mart host: <a href="http://www.ensembl.org:80/biomart/martservice" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice\46sa\75D\46sntz\0751\46usg\75AFQjCNF84P8pBVtfNkFTkCUKHEj3h9pmqg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice\46sa\75D\46sntz\0751\46usg\75AFQjCNF84P8pBVtfNkFTkCUKHEj3h9pmqg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice
Checking attributes ...Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=attributes&amp;dataset=hsapiens_gene_ensembl&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL&amp;virtualSchema=default" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dattributes%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNEtwNks0lYT2v3Qu2Mw-Pq9ScwBtg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dattributes%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNEtwNks0lYT2v3Qu2Mw-Pq9ScwBtg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=attributes&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok
Checking filters ...Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=filters&amp;dataset=hsapiens_gene_ensembl&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL&amp;virtualSchema=default" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dfilters%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNFxYfZxx_krcpWU2b7JQyxMLb-2AQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dfilters%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNFxYfZxx_krcpWU2b7JQyxMLb-2AQ&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=filters&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok
> mousegenes <-getLDS(attributes = c("ensembl_gene_id"), filters = "refseq_mrna", values = c("NM_016607","NM_022838","NM_001668"), mart = human, attributesL = c("ensembl_gene_id"), martL = mouse, verbose = TRUE)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= "biomaRt"> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Filter name = 'refseq_mrna' value = 'NM_016607,NM_022838,NM_001668' /></Dataset><Dataset name = 'mmusculus_gene_ensembl' ><Attribute name = 'ensembl_gene_id'/></Dataset></Query>
> mousegenes
  <a href="http://Ensembl.Gene.ID" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2FEnsembl.Gene.ID\46sa\75D\46sntz\0751\46usg\75AFQjCNGq2vNyxAhBs48eK4ReBY82oePN8Q&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2FEnsembl.Gene.ID\46sa\75D\46sntz\0751\46usg\75AFQjCNGq2vNyxAhBs48eK4ReBY82oePN8Q&#39;;return true;">Ensembl.Gene.ID  Ensembl.Gene.ID.1
1 ENSG00000125962 ENSMUSG00000072969
2 ENSG00000102401 ENSMUSG00000049047
3 ENSG00000143437 ENSMUSG00000015522

Maybe it was an internet connection glitch or the server was really busy.
Hope this helps,
Best Regards,
Thomas
On 21 Mar 2016, at 07:18, Darya Vanichkina <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="nBWrrSjRKgAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">d.vani...@...> wrote:

Hi! I'm having trouble once again running code that successfully worked last week (!). 

Briefly, I am trying to convert a list of human refseq mRNA gene identifiers to mouse ENSMG gene names. The commands and tracebacks I am using are the following:

library(biomaRt)
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", verbose = TRUE)

Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=version&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dversion%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL\46sa\75D\46sntz\0751\46usg\75AFQjCNGKpzSHsLMlFq5HOkWjmDhGz4UU5A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dversion%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL\46sa\75D\46sntz\0751\46usg\75AFQjCNGKpzSHsLMlFq5HOkWjmDhGz4UU5A&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Mart host: <a href="http://www.ensembl.org:80/biomart/martservice" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice\46sa\75D\46sntz\0751\46usg\75AFQjCNF84P8pBVtfNkFTkCUKHEj3h9pmqg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice\46sa\75D\46sntz\0751\46usg\75AFQjCNF84P8pBVtfNkFTkCUKHEj3h9pmqg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice
Checking attributes ...Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=attributes&amp;dataset=hsapiens_gene_ensembl&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL&amp;virtualSchema=default" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dattributes%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNEtwNks0lYT2v3Qu2Mw-Pq9ScwBtg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dattributes%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNEtwNks0lYT2v3Qu2Mw-Pq9ScwBtg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=attributes&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok
Checking filters ...Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=filters&amp;dataset=hsapiens_gene_ensembl&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL&amp;virtualSchema=default" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dfilters%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNFxYfZxx_krcpWU2b7JQyxMLb-2AQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dfilters%26dataset%3Dhsapiens_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNFxYfZxx_krcpWU2b7JQyxMLb-2AQ&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=filters&dataset=hsapiens_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok

mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl", verbose = TRUE)
Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=version&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dversion%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL\46sa\75D\46sntz\0751\46usg\75AFQjCNGKpzSHsLMlFq5HOkWjmDhGz4UU5A&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dversion%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL\46sa\75D\46sntz\0751\46usg\75AFQjCNGKpzSHsLMlFq5HOkWjmDhGz4UU5A&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
   V1
1 0.7
BioMartServer running BioMart version: 0.7
Mart virtual schema: default
Mart host: <a href="http://www.ensembl.org:80/biomart/martservice" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice\46sa\75D\46sntz\0751\46usg\75AFQjCNF84P8pBVtfNkFTkCUKHEj3h9pmqg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice\46sa\75D\46sntz\0751\46usg\75AFQjCNF84P8pBVtfNkFTkCUKHEj3h9pmqg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice
Checking attributes ...Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=attributes&amp;dataset=mmusculus_gene_ensembl&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL&amp;virtualSchema=default" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dattributes%26dataset%3Dmmusculus_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNHmIuwaUDVM82671RLYatoIl2q7Uw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dattributes%26dataset%3Dmmusculus_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNHmIuwaUDVM82671RLYatoIl2q7Uw&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=attributes&dataset=mmusculus_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok
Checking filters ...Attempting web service request:
<a href="http://www.ensembl.org:80/biomart/martservice?type=filters&amp;dataset=mmusculus_gene_ensembl&amp;requestid=biomaRt&amp;mart=ENSEMBL_MART_ENSEMBL&amp;virtualSchema=default" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dfilters%26dataset%3Dmmusculus_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNFjI79fs5Y6l1blVvTl1kSsWzeshg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dfilters%26dataset%3Dmmusculus_gene_ensembl%26requestid%3DbiomaRt%26mart%3DENSEMBL_MART_ENSEMBL%26virtualSchema%3Ddefault\46sa\75D\46sntz\0751\46usg\75AFQjCNFjI79fs5Y6l1blVvTl1kSsWzeshg&#39;;return true;">http://www.ensembl.org:80/biomart/martservice?type=filters&dataset=mmusculus_gene_ensembl&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL&virtualSchema=default
 ok

mousegenes <-getLDS(attributes = c("ensembl_gene_id"), filters = "refseq_mrna", values = c("NM_016607","NM_022838","NM_001668"), mart = human, attributesL = c("ensembl_gene_id"), martL = mouse, verbose = TRUE)

<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= "biomaRt"> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'ensembl_gene_id'/><Filter name = 'refseq_mrna' value = 'NM_016607,NM_022838,NM_001668' /></Dataset><Dataset name = 'mmusculus_gene_ensembl' ><Attribute name = 'ensembl_gene_id'/></Dataset></Query>
Error: Expectation Failed

traceback()

4: stop(err)
3: stop.if.HTTP.error(http.header)
2: postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery)
1: getLDS(attributes = c("ensembl_gene_id"), filters = "refseq_mrna", 
       values = c("NM_016607", "NM_022838", "NM_001668"), mart = human, 
       attributesL = c("ensembl_gene_id"), martL = mouse, verbose = TRUE)

sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] genefilter_1.52.1          plyr_1.8.3                 hwriter_1.3.2              gplots_2.17.0             
 [5] DESeq2_1.10.1              RcppArmadillo_0.6.500.4.0  Rcpp_0.12.3                SummarizedExperiment_1.0.2
 [9] Biobase_2.30.0             GenomicRanges_1.22.4       GenomeInfoDb_1.6.3         IRanges_2.4.8             
[13] S4Vectors_0.8.11           BiocGenerics_0.16.1        gridExtra_2.2.1            biomaRt_2.26.1            
[17] edgeR_3.12.0               limma_3.26.8               reshape2_1.4.1             RColorBrewer_1.1-2        
[21] data.table_1.9.6           ggplot2_2.1.0             

loaded via a namespace (and not attached):
 [1] gtools_3.5.0         locfit_1.5-9.1       splines_3.2.3        lattice_0.20-33      colorspace_1.2-6    
 [6] chron_2.3-47         XML_3.98-1.4         survival_2.38-3      foreign_0.8-66       DBI_0.3.1           
[11] BiocParallel_1.4.3   lambda.r_1.1.7       stringr_1.0.0        zlibbioc_1.16.0      munsell_0.4.3       
[16] gtable_0.2.0         futile.logger_1.4.1  caTools_1.17.1       labeling_0.3         latticeExtra_0.6-28 
[21] geneplotter_1.48.0   AnnotationDbi_1.32.3 KernSmooth_2.23-15   acepack_1.3-3.3      xtable_1.8-2        
[26] scales_0.4.0         gdata_2.17.0         Hmisc_3.17-2         annotate_1.48.0      XVector_0.10.0      
[31] digest_0.6.9         stringi_1.0-1        grid_3.2.3           tools_3.2.3          bitops_1.0-6        
[36] magrittr_1.5         RCurl_1.95-4.8       RSQLite_1.0.0        Formula_1.2-1        cluster_2.0.3       
[41] futile.options_1.0.0 rpart_4.1-10         nnet_7.3-12   


Why has my command stopped working???

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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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