Question: Using mgeneSim with Ensembl ids
gravatar for saadmurtazakhan
22 months ago by
United States
saadmurtazakhan10 wrote:

I have a list of Ensembl ids that I am trying to use with mgeneSim function. Everytime I run it it returns a 0X0 matrix with the following warning message :- 

1: In : applied to non-(list or vector) of type 'NULL'

Here is the code that I use :-

mytestgenes <- c("ENSG00000271793","ENSG00000172789","ENSG00000264364","ENSG00000120533","ENSG00000174871","ENSG00000112531")

GOsim_matrix <- mgeneSim(genes=mytestgenes,ont="MF",organism="human",measure="Wang",verbose=T)

I am assuming that GOsemsim only works with enrez ids and I was wondering if there is a way to make it work with Ensembl ids.



ADD COMMENTlink modified 22 months ago by Guangchuang Yu990 • written 22 months ago by saadmurtazakhan10
gravatar for Guangchuang Yu
22 months ago by
Hong Kong
Guangchuang Yu990 wrote:

this was supported in devel branch. see the vignette

ADD COMMENTlink written 22 months ago by Guangchuang Yu990

This is my session info.

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GOSemSim_1.30.3      BiocInstaller_1.22.3

loaded via a namespace (and not attached):
 [1]   IRanges_2.6.1        parallel_3.3.0      
 [4] DBI_0.4-1            tools_3.3.0          Rcpp_0.12.6         
 [7] Biobase_2.32.0       AnnotationDbi_1.34.4 RSQLite_1.0.0       
[10] S4Vectors_0.10.2     BiocGenerics_0.18.0  stats4_3.3.0        
[13] GO.db_3.3.0         

What version of R would you think would work with that given in the vignette. 


PS: I dont have admin priveleges

ADD REPLYlink modified 22 months ago • written 22 months ago by saadmurtazakhan10

if you have no idea how to install devel branch, I recommend you stick with release branch.


Instead you can convert ensemble id to entrez gene id (e.g. using bitr).

ADD REPLYlink written 22 months ago by Guangchuang Yu990

What should I change below to make bitr work.

bitr(mytestgenes, fromType="ENSEMBLID", toType="ENTREZID", OrgDb="")
Error in bitr(mytestgenes, fromType = "ENSEMBLID", toType = "ENTREZID",  : 
  unused argument (OrgDb = "")
ADD REPLYlink written 22 months ago by saadmurtazakhan10

pls make sure clusterProfiler was loaded correctly and you are using the latest release version.

ADD REPLYlink written 22 months ago by Guangchuang Yu990
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