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Hi!
I am facing an issue with biomaRt.I have tried posting this on Bioconductor support as well. I'm working behind a proxy and have modified the Renviron file to incorporate the proxy addresses and port. I have also used the RCurlOptions to feed in the proxy as suggested in the biomart vignette. I am using the useMart command as:
ensembl<-useMart("ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", + host="www.ensembl.org")
which doesn't throw any error. listMarts and listAttributes, everything works fine but when I actually come to getBM the connection is refused. The command that I'm using is (I'm following DESeq2 beginner's guide)
genemap<-getBM(attributes=c("entrezgene", "ensembl_gene_id", + "mgi_symbol"), filters="ensembl_gene_id", + values=res24$ensembl, mart=ensembl) Error in value[3L] : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
I can connect to ensembl and access the data on its ftp servers through browser.
Any suggestions will be much appreciated. Thanks!
sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie)
locale: [1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] RCurl_1.95-4.8 bitops_1.0-6
[3] biomaRt_2.26.1 DESeq2_1.10.1
[5] RcppArmadillo_0.6.600.4.0 Rcpp_0.12.4
[7] SummarizedExperiment_1.0.2 Biobase_2.30.0
[9] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3
[11] IRanges_2.4.8 S4Vectors_0.8.11
[13] BiocGenerics_0.16.1
loaded via a namespace (and not attached): [1] RColorBrewer_1.1-2 futile.logger_1.4.1 plyr_1.8.3
[4] XVector_0.10.0 futile.options_1.0.0 zlibbioc_1.16.0
[7] rpart_4.1-10 RSQLite_1.0.0 annotate_1.48.0
[10] gtable_0.2.0 lattice_0.20-33 DBI_0.3.1
[13] gridExtra_2.2.1 genefilter_1.52.1 cluster_2.0.3
[16] locfit_1.5-9.1 grid_3.2.3 nnet_7.3-12
[19] AnnotationDbi_1.32.3 XML_3.98-1.4 survival_2.38-3
[22] BiocParallel_1.4.3 foreign_0.8-66 latticeExtra_0.6-28 [25] Formula_1.2-1 geneplotter_1.48.0 ggplot2_2.1.0
[28] lambda.r_1.1.7 Hmisc_3.17-2 scales_0.4.0
[31] splines_3.2.3 colorspace_1.2-6 xtable_1.8-2
[34] acepack_1.3-3.3 munsell_0.4.3
I am facing an issue with biomaRt.I have tried posting this on Bioconductor support as well. I'm working behind a proxy and have modified the Renviron file to incorporate the proxy addresses and port. I have also used the RCurlOptions to feed in the proxy as suggested in the biomart vignette. I am using the useMart command as:
ensembl<-useMart("ENSEMBL_MART_ENSEMBL", dataset="mmusculus_gene_ensembl", + host="www.ensembl.org")
which doesn't throw any error. listMarts and listAttributes, everything works fine but when I actually come to getBM the connection is refused. The command that I'm using is (I'm following DESeq2 beginner's guide)
genemap<-getBM(attributes=c("entrezgene", "ensembl_gene_id", + "mgi_symbol"), filters="ensembl_gene_id", + values=res24$ensembl, mart=ensembl) Error in value[3L] : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
I can connect to ensembl and access the data on its ftp servers through browser.
Any suggestions will be much appreciated. Thanks!
sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie)
locale: [1] LC_CTYPE=en_IN LC_NUMERIC=C LC_TIME=en_IN
[4] LC_COLLATE=en_IN LC_MONETARY=en_IN LC_MESSAGES=en_IN
[7] LC_PAPER=en_IN LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base
other attached packages: [1] RCurl_1.95-4.8 bitops_1.0-6
[3] biomaRt_2.26.1 DESeq2_1.10.1
[5] RcppArmadillo_0.6.600.4.0 Rcpp_0.12.4
[7] SummarizedExperiment_1.0.2 Biobase_2.30.0
[9] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3
[11] IRanges_2.4.8 S4Vectors_0.8.11
[13] BiocGenerics_0.16.1
loaded via a namespace (and not attached): [1] RColorBrewer_1.1-2 futile.logger_1.4.1 plyr_1.8.3
[4] XVector_0.10.0 futile.options_1.0.0 zlibbioc_1.16.0
[7] rpart_4.1-10 RSQLite_1.0.0 annotate_1.48.0
[10] gtable_0.2.0 lattice_0.20-33 DBI_0.3.1
[13] gridExtra_2.2.1 genefilter_1.52.1 cluster_2.0.3
[16] locfit_1.5-9.1 grid_3.2.3 nnet_7.3-12
[19] AnnotationDbi_1.32.3 XML_3.98-1.4 survival_2.38-3
[22] BiocParallel_1.4.3 foreign_0.8-66 latticeExtra_0.6-28 [25] Formula_1.2-1 geneplotter_1.48.0 ggplot2_2.1.0
[28] lambda.r_1.1.7 Hmisc_3.17-2 scales_0.4.0
[31] splines_3.2.3 colorspace_1.2-6 xtable_1.8-2
[34] acepack_1.3-3.3 munsell_0.4.3