Gprofiler issues on organism input in gost function

Question

[ilaria]

Hi!

I'm trying to convert a list of differentially expressed genes, from gene _id (ex: MGG_xx) using gost function (gprofiler) to get the GO. The reference organism (Pyricularia oryzae 70-15) is supposed to be inside gprofiler, but I'm getting trouble defining the organism in the function.

Here the script I'm using:

library(gprofiler2)
library(dplyr)

genelist<-as.vector(rownames(deg))
View(genelist)

gostres <- gost(query = genelist, organism = "poryzae70-15", ordered_query = FALSE, 
                multi_query = FALSE, significant = TRUE, exclude_iea = FALSE, 
                measure_underrepresentation = FALSE, evcodes = TRUE, 
                user_threshold = 0.05, correction_method = "g_SCS", 
                domain_scope = "annotated", custom_bg = NULL, 
                numeric_ns = "", sources = NULL)

The error I'm getting is the following, and it is the same no matter the entry I use in organism:

Error in gost(query = genelist, organism = "poryzae70-15", ordered_query = FALSE,  : 
  Bad request, response code 400

Did anyone face the same issue before? Any suggestion to solve it? Thanks!

[lieven.sterck]

hi ilaria,

Welcome to the forum.

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[ilaria]

Sure, thak you!

[Jeremy]

I know this doesn't address your error, but could you use the g:Profiler website instead of using R?

[ilaria]

I was actually trying in R, of course, the website query worked. Anyway, I was able to discover the id species right through the website query! So I could work in R.

Answer 1

[hedi.peterson]

Hi Ilaria,

With the random gene IDs of your organism the query seems to work fine. In case you still have trouble getting the results, please contact us at [e-mail] or via the contact form on our website https://biit.cs.ut.ee/gprofiler/page/contact. It would be beneficial if you add an example of your input so that we could investigate it further.

On behalf of the g:Profiler team, Hedi.