GO analysis in R vs website
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Entering edit mode
Nitro • 0
@5869f5e2
Last seen 5 days 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"),

Thanks a lot !

GO RNASeq • 63 views
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Entering edit mode
@james-w-macdonald-5106
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.

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