Hi,
I'm searching for all ENSEMBL gene IDs associated with a particular GO ID (GO:0065005), which - using biomaRt - returns a single gene. I do:
library(biomaRt) ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") out <- getBM(attributes=c('ensembl_gene_id', 'go_id'),filters = 'go', values = 'GO:0065005', mart = ensembl) unique(out$ensembl_gene_id) [1] "ENSG00000110244"
However, when use the biomart website to run the same query I get results for 36 genes. Here are links to images of the query I used:
https://drive.google.com/open?id=17GSR8JdZuOzcc8ScxMTjFTexQgeE_Xi-
The results in the browser:
https://drive.google.com/open?id=1j1CRz5AEDB7_SICob1qlM5SAkUYsEneO
And the results file itself:
https://drive.google.com/open?id=1ppbOnNilrTGiZY6o_q-X_ue-MAXMrTOA
Can anyone suggest a reason for this?
Dan
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sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.34.2 loaded via a namespace (and not attached): [1] Rcpp_0.12.16 AnnotationDbi_1.40.0 magrittr_1.5 [4] BiocGenerics_0.24.0 progress_1.1.2 IRanges_2.12.0 [7] bit_1.1-12 R6_2.2.2 httr_1.3.1 [10] stringr_1.3.0 blob_1.1.1 tools_3.4.3 [13] parallel_3.4.3 Biobase_2.38.0 DBI_0.8 [16] bit64_0.9-7 digest_0.6.15 assertthat_0.2.0 [19] S4Vectors_0.16.0 bitops_1.0-6 curl_3.2 [22] RCurl_1.95-4.10 memoise_1.1.0 RSQLite_2.1.0 [25] stringi_1.1.7 compiler_3.4.3 prettyunits_1.0.2 [28] stats4_3.4.3 XML_3.98-1.10
Thanks very much Mike, this solved my problem!
Dan