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!
1 answer
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 biit.support@ut.ee 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.
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hi ilaria,
Welcome to the forum.
Please use the formatting bar (especially the
codeoption) to present your post better. I've done it for you this time.Thank you!
Sure, thak you!
I know this doesn't address your error, but could you use the g:Profiler website instead of using R?
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.