GO analysis in R vs website
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Entering edit mode
Nitro • 0
@5869f5e2
Last seen 13 months ago
Belgium

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 ? 

```r

GO_Analysis=gost(query=Result_table_B_ASHR$ID, 
                 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 • 715 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 7 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.

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

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