I am trying to find orthologs between a variety of plant and animal species, including Arabidopsis thaliana and humans. When I try to use getLDS with both the Arabidopsis genes dataset from the plants_mart at plants.ensembl.org and the human genes dataset at ensembl.org, I get an error saying that the Arabidopsis gene dataset was not found. I am reasonably confident that this is due to the fact that the two marts have different hosts, and am prepared to hear that I just can't execute getLDS on two marts with different hosts, but I figured that I would ask and see if I was missing something, just in case.
> library("biomaRt") > ensembl = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl") > plants = useMart("plants_mart", host="plants.ensembl.org", dataset="athaliana_eg_gene") > getLDS(attributes="ensembl_gene_id", mart=ensembl, attributesL="ensembl_gene_id", martL=plants) Error in getLDS(attributes = "ensembl_gene_id", mart = ensembl, attributesL = "ensembl_gene_id", : Query ERROR: caught BioMart::Exception::Usage: WITHIN Virtual Schema : default, Dataset athaliana_eg_gene NOT FOUND > listDatasets(plants)[3:3,1]  "athaliana_eg_gene"
> sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.5 (Final) Matrix products: default BLAS/LAPACK: /cm/shared/apps/OpenBLAS/current/lib/libopenblas_sandybridgep-r0.2.14.so locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  biomaRt_2.36.1 loaded via a namespace (and not attached):  Rcpp_0.12.17 AnnotationDbi_1.42.1 magrittr_1.5  BiocGenerics_0.26.0 hms_0.4.2 progress_1.2.0  IRanges_2.14.10 bit_1.1-14 R6_2.2.2  rlang_0.2.1 httr_1.3.1 stringr_1.3.1  blob_1.1.1 tools_3.5.0 parallel_3.5.0  Biobase_2.40.0 DBI_1.0.0 bit64_0.9-7  digest_0.6.15 assertthat_0.2.0 crayon_1.3.4  S4Vectors_0.18.3 bitops_1.0-6 curl_3.2  RCurl_1.95-4.10 memoise_1.1.0 RSQLite_2.1.1  stringi_1.2.3 compiler_3.5.0 prettyunits_1.0.2  stats4_3.5.0 XML_3.98-1.11 pkgconfig_2.0.1