Does EnrichmentBrowser package support analysis of RNA-seq data from Oryza sativa (rice)?
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sjw • 0
@fef88af9
Last seen 3.0 years ago
Germany

I would like to use the EnrichmentBrowser package to perform enrichment analysis on my RNA-seq gene expression data from Oryza sativa japonica.

In order to determine the correct organism code to use in EnrichmentBrowser, I followed the link (https://www.genome.jp/kegg/catalog/org_list.html) in the EnrichmentBrowser v2.22 manual (https://bioconductor.org/packages/release/bioc/manuals/EnrichmentBrowser/man/EnrichmentBrowser.pdf) to the KEGG genomes page. On the KEGG page I found two possible codes for Oryza sativa japonica, "osa" and "dosa"

I get the same unrecognized organism ID error when I use either of those organism codes

> idTypes("osa")
Error in .org2pkg(anno) : unrecognized organism ID 'osa'
> idTypes("dosa")
Error in .org2pkg(anno) : unrecognized organism ID 'dosa'

However, when I check for idTypes with organism code "mmu" (for Mus musculus (mouse)), I am prompted to install the necessary annotation. If I decline to install it now, then I am told that the necessary annotation package is not availible. This is a different error than I get with the rice organism codes from KEGG (see above), and suggests to me that the error I get with idTypes("osa") cannot be resolved by installing the relevant annotation package for rice.

> idTypes("mmu")
Corresponding annotation package not found: org.Mm.eg.db
Make sure that you have it installed.
Install it now? (y/n): n
Error in isAvailable(anno.pkg) : Package org.Mm.eg.db is not available

I also work with datasets from Arabidopsis, and I already have the org.At.tair.db package installed. when I check for idTypes with organism code "ath" (for Arabidopsis thaliana), I do not get an error of any kind, and the idTypes available in EnrichmentBrowser for Arabidopsis are returned/

> idTypes("ath")

 [1] "ARACYC"       "ARACYCENZYME" "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"     "GO"          
 [9] "GOALL"        "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PMID"         "REFSEQ"       "SYMBOL"       "TAIR"

Does EnrichmentBrowser package support Oryza sativa (rice)?

```

sessionInfo() R version 4.1.0 (2021-05-18) 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] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] org.Hs.eg.db_3.13.0 AnnotationDbi_1.54.1 DESeq2_1.32.0 EnrichmentBrowser_2.22.0
[5] graph_1.70.0 SummarizedExperiment_1.22.0 Biobase_2.52.0 GenomicRanges_1.44.0
[9] GenomeInfoDb_1.28.0 IRanges_2.26.0 S4Vectors_0.30.0 BiocGenerics_0.38.0
[13] MatrixGenerics_1.4.0 matrixStats_0.59.0

loaded via a namespace (and not attached): [1] httr_1.4.2 edgeR_3.34.0 bit64_4.0.5 splines_4.1.0 assertthat_0.2.1
[6] blob_1.2.1 GenomeInfoDbData_1.2.6 pillar_1.6.1 RSQLite_2.2.7 lattice_0.20-44
[11] glue_1.4.2 limma_3.48.0 RColorBrewer_1.1-2 XVector_0.32.0 colorspace_2.0-1
[16] Matrix_1.3-4 GSEABase_1.54.0 XML_3.99-0.6 pkgconfig_2.0.3 genefilter_1.74.0
[21] zlibbioc_1.38.0 purrr_0.3.4 xtable_1.8-4 scales_1.1.1 BiocParallel_1.26.0
[26] tibble_3.1.2 annotate_1.70.0 KEGGREST_1.32.0 generics_0.1.0 ggplot2_3.3.5
[31] ellipsis_0.3.2 cachem_1.0.5 survival_3.2-11 magrittr_2.0.1 crayon_1.4.1
[36] memoise_2.0.0 KEGGgraph_1.52.0 fansi_0.5.0 tools_4.1.0 lifecycle_1.0.0
[41] munsell_0.5.0 locfit_1.5-9.4 DelayedArray_0.18.0 Biostrings_2.60.1 compiler_4.1.0
[46] rlang_0.4.11 grid_4.1.0 RCurl_1.98-1.3 rstudioapi_0.13 bitops_1.0-7
[51] gtable_0.3.0 DBI_1.1.1 R6_2.5.0 dplyr_1.0.7 fastmap_1.1.0
[56] bit_4.0.4 utf8_1.2.1 Rgraphviz_2.36.0 Rcpp_1.0.6 vctrs_0.3.8
[61] geneplotter_1.70.0 png_0.1-7 tidyselect_1.1.1

EnrichmentBrowser Oryza_sativa • 727 views
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