Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • biomaRt not connecting behind proxy

    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

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
66 views
0 likes
Last Post seqadmin  
Working...
X