Hello,

I would like to apply package ‘GOsummaries’  to my dataset. I set up my analysis following the instruction with one exception. I used EntrezIDs instead of ProbeIDs.

I have  two lists of EntrezIDs (e.g.) :

list1:

head(list1)
[1] "100302592" "27215"     "378954"    "100503548" "245536"    "327768"  

list2 :

head(list2)
[1] "333883" "11801" "667410" "16186" "100316689" "380654"  

gl = list(List = list(list1, list2))

str(gl)
List of 1
 $ List:List of 2
  ..$ : chr [1:15] "100302592" "27215" "378954" "100503548" ...
  ..$ : chr [1:8] "333883" "11801" "667410" "16186" ...

gs = gosummaries(gl, organism = "mmusculus")
Error in data.frame(Query = NA, gpr) : 
  arguments imply differing number of rows: 1, 0

I am wondering if ‘GOsummaries’ works with 'EntrezIDs as well.

Thanks for your help.

Anita

GOsummaries actually can handle the Entrez ids as well, although the feature is not well documented. With the numeric IDs gProfiler (http://biit.cs.ut.ee/gprofiler/) that is used by GOsummaries does not know to which database these IDs correspond to, but you can specify it from the web interface. The same parameter can be passed through GOsummaries as well. So for your case something as follows would work:

gs = gosummaries(gl, organism = "mmusculus", numeric_ns = "ENTREZGENE_ACC")

If you have some other numeric id-s you can check if your identifier source is in the options in the g:Profiler web interface. 

Hi Raivo, 

​Thank you for your help. 

Anita