GO analysis in R vs website
Entering edit mode
Nitro • 0
Last seen 5 days ago

Hi all,

I'm trying to do a Gene Ontology with the Gost function. I'm working on sheep, which I believe can be referred to as "oaries" or "oarambouillet".

I'm facing a bit of an issue, as when I'm trying to run the gost I get this error:

```rNo results to show Please make sure that the organism is correct or set significant = FALSE

I've tried both organisms, as well as setting significant to false, but it's not working. One funny bit though is that if I ask the function to generate a short link, the query runs on the GO website.

Does anyone knows why it runs on the website but not in R ? 


                 organism =  "oaries",
                 ordered_query = TRUE,
                 multi_query = FALSE, 
                 significant = TRUE,
                 exclude_iea = FALSE,
                 measure_underrepresentation = FALSE,
                 evcodes = TRUE, 
                 domain_scope = "known", 
                 correction_method = "fdr", 
                 user_threshold = 0.05, 
                 custom_bg = NULL, 
                 numeric_ns = "ENTREZGENE_ACC",
                 sources =c("GO:MF","GO:BP","KEGG", "GO:CC"),
                 as_short_link = FALSE)

Thanks a lot !
GO RNASeq • 63 views
Entering edit mode
Last seen 5 hours ago
United States

It appears you are using the CRAN gprofiler2 package, which is not a Bioconductor package. This site is meant to support Bioconductor packages, so your question is off topic. You might try biostars.org instead.

Entering edit mode

Oh OK sorry about that, thank you for your response James :)


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