Hi there. I'm so sorry to bring up an old error, but for some reason, I just can't get this query to work! I've tried substituting in different Zea mays gene names in "values", trying one attribute at a time in "attributes", and various different "filters". My gene names come from a STAR alignment to the Zm-B73 reference genome.
mart <- useMart(biomart = "phytozome_mart",
dataset = "phytozome",
host = "https://phytozome.jgi.doe.gov")
b <- getBM(
attributes=c('gene_name1','organism_name','gene_description', 'peptide_name','kog_desc','go_desc'),
filters="gene_name_filter",
values="Zm00001eb069270",
mart=mart)
Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, :
The query to the BioMart webservice returned an invalid result.
The number of columns in the result table does not equal the number of attributes in the query.
Please report this on the support site at http://support.bioconductor.org
sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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_2.50.1 BiocManager_1.30.16
loaded via a namespace (and not attached):
[1] KEGGREST_1.34.0 progress_1.2.2 tidyselect_1.1.1
[4] purrr_0.3.4 vctrs_0.3.8 generics_0.1.1
[7] stats4_4.1.2 BiocFileCache_2.2.0 utf8_1.2.2
[10] blob_1.2.2 XML_3.99-0.8 rlang_0.4.12
[13] pillar_1.6.4 withr_2.4.3 glue_1.6.0
[16] DBI_1.1.2 rappdirs_0.3.3 BiocGenerics_0.40.0
[19] bit64_4.0.5 dbplyr_2.1.1 lambda.r_1.2.4
[22] GenomeInfoDbData_1.2.7 lifecycle_1.0.1 stringr_1.4.0
[25] zlibbioc_1.40.0 Biostrings_2.62.0 futile.logger_1.4.3
[28] memoise_2.0.1 Biobase_2.54.0 IRanges_2.28.0
[31] fastmap_1.1.0 GenomeInfoDb_1.30.0 curl_4.3.2
[34] AnnotationDbi_1.56.2 fansi_1.0.0 Rcpp_1.0.7
[37] formatR_1.11 filelock_1.0.2 cachem_1.0.6
[40] S4Vectors_0.32.3 XVector_0.34.0 bit_4.0.4
[43] hms_1.1.1 png_0.1-7 digest_0.6.29
[46] stringi_1.7.6 dplyr_1.0.7 tools_4.1.2
[49] bitops_1.0-7 magrittr_2.0.1 RCurl_1.98-1.5
[52] RSQLite_2.2.9 tibble_3.1.6 futile.options_1.0.1
[55] crayon_1.4.2 pkgconfig_2.0.3 ellipsis_0.3.2
[58] xml2_1.3.3 prettyunits_1.1.1 assertthat_0.2.1
[61] httr_1.4.2 R6_2.5.1 compiler_4.1.2
Thanks! I knew it was something like that.
It worked perfectly for mine!