Anyone that could give me an example for GO annotation of species Rice with an R package. My rice ID is like "LOC_Os01g01312". It's a location ID. Thanks.
Were you able to figure this out? I am experiencing a similar challenge
Hi @djyjin and rohitsatyam102
I have also been facing challenges while conducting goseq analysis in R. I have obtained DEGs from rice samples, including gene ID, logFC, and adjusted p-value. I am using the script mentioned below. However, since this script requires the rice dataset (rg.Os.eg.db) and I cannot find this dataset in BiocManager or BiomaRt, I am unable to complete my analysis. :(
I was wondering if you have already found a way to perform the goseq analysis that you could share with me, please?
I hope this message finds you well. Have a nice day!
Rice genome annotation project has moved to http://rice.uga.edu/. Since Rice used those project specific ID's your best bet may be to get the GO annotation from http://rice.uga.edu/annotation_pseudo_goslim.shtml
You can email the site maintainers to see if there is a way to download the GO terms for all rice proteins.
Thanks a lot for your response!
You are correct that I can have GO terms from Rice genome annotation project and I already have them. Still I have been trying to get the GO pathways through goseq analysis since in most of the articles they mentioned using R packages instead of RAP-DB
That is why I was asking for the rice annotation packages to use in R. :,)
Check out this paper : http://nar.oxfordjournals.org/content/early/2013/04/29/nar.gkt281.full
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