Is the Ensemble server down? Using biomaRt, I get back internal server errors and the suggestion that I use other mirrors, at no avail. The BioMart service was actually down for a while today, i noticed, but I believe all should now be fine as it is up again. However, biomaRt is not able to access it.
sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.1.1
Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale: [1] C
time zone: Europe/Amsterdam tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] biomaRt_2.58.0 DESeq2_1.42.0
[3] SummarizedExperiment_1.32.0 Biobase_2.62.0
[5] MatrixGenerics_1.14.0 matrixStats_1.1.0
[7] GenomicRanges_1.54.1 GenomeInfoDb_1.38.1
[9] IRanges_2.36.0 S4Vectors_0.40.2
[11] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] KEGGREST_1.42.0 gtable_0.3.4 ggplot2_3.4.4
[4] lattice_0.22-5 vctrs_0.6.4 tools_4.3.2
[7] bitops_1.0-7 generics_0.1.3 curl_5.1.0
[10] parallel_4.3.2 tibble_3.2.1 fansi_1.0.5
[13] AnnotationDbi_1.64.1 RSQLite_2.3.3 blob_1.2.4
[16] pkgconfig_2.0.3 Matrix_1.6-3 dbplyr_2.4.0
[19] lifecycle_1.0.4 GenomeInfoDbData_1.2.11 stringr_1.5.1
[22] compiler_4.3.2 progress_1.2.2 Biostrings_2.70.1
[25] munsell_0.5.0 codetools_0.2-19 RCurl_1.98-1.13
[28] pillar_1.9.0 crayon_1.5.2 BiocParallel_1.36.0
[31] DelayedArray_0.28.0 cachem_1.0.8 abind_1.4-5
[34] digest_0.6.33 tidyselect_1.2.0 locfit_1.5-9.8
[37] stringi_1.8.2 purrr_1.0.2 dplyr_1.1.4
[40] fastmap_1.1.1 grid_4.3.2 colorspace_2.1-0
[43] cli_3.6.1 SparseArray_1.2.2 magrittr_2.0.3
[46] S4Arrays_1.2.0 XML_3.99-0.15 utf8_1.2.4
[49] withr_2.5.2 rappdirs_0.3.3 filelock_1.0.2
[52] prettyunits_1.2.0 scales_1.2.1 bit64_4.0.5
[55] XVector_0.42.0 httr_1.4.7 bit_4.0.5
[58] hms_1.1.3 png_0.1-8 memoise_2.0.1
[61] BiocFileCache_2.10.1 rlang_1.1.2 Rcpp_1.0.11
[64] glue_1.6.2 DBI_1.1.3 xml2_1.3.5
[67] R6_2.5.1 zlibbioc_1.48.0
It was down around that time - I know because I was also using it. As per James, just re-try to make the connection with the server.
Well, I keep getting messages that servers are unresponsive. None of the mirrors work, and messages suggest its on their end, not mine ('Ensembl site unresponsive,[...]').
Yup, they seem to be down. What exactly are you trying to do? There may be other options.
I want to link 'external_gene_names' (mouse, multiple lists) with the ensembl gene IDs and HGNC symbols of human orthologues using getLDS(). I see that getBM() in biomaRt now works (wasn't the case this afternoon), so there's hope!
I'm beginning to think it is an issue with getLDS(). getBM() just works like a charm, but linking datasets (mouse <-> man) still throws up 'internal sever errors'. I have confirmation from Ensembl that there are problems on their end that they hope to resolve them as soon as possible.
What are the mouse IDs? There is an
Orthology.eg.db
package that can be used to map mouse NCBI Gene IDs to human, and you can use the human and mouseOrgDb
packages to get the symbols. It might be simpler to take that route, particularly if you don't already have Ensembl IDs.Thanks, I'm now exploring these. I want to map external gene names (long lists, actually) to human HGNC symbols and Ensembl gene IDs...
Yes, you have already said that. The length of the lists isn't material to this discussion, but the nature of the IDs is. I have no idea what an 'external gene name' might be, and unless you want to provide that information I am afraid nobody will be able to give you any more help.
"external_gene_name" is a biomaRt attribute for mouse gene names, equivalent but (obviously) not identical to human HGNC symbols.
I normally caution against mapping between annotation sources (NCBI and Ensembl), as it usually doesn't work well. However, it is possible.
Thank you James, very useful!!!