Entering edit mode
Hi,
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 is.na(go) : is.na() 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.
regards
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)
locale:
[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] org.Hs.eg.db_3.3.0 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
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).
What should I change below to make bitr work.
pls make sure clusterProfiler was loaded correctly and you are using the latest release version.