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Question: Using mgeneSim with Ensembl ids
0
gravatar for saadmurtazakhan
15 months ago by
United States
saadmurtazakhan10 wrote:
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

ADD COMMENTlink modified 15 months ago by Guangchuang Yu800 • written 15 months ago by saadmurtazakhan10
0
gravatar for Guangchuang Yu
15 months ago by
Hong Kong
Guangchuang Yu800 wrote:

this was supported in devel branch. see the vignette https://bioconductor.org/packages/devel/bioc/vignettes/GOSemSim/inst/doc/GOSemSim.html

ADD COMMENTlink written 15 months ago by Guangchuang Yu800

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

ADD REPLYlink modified 15 months ago • written 15 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 15 months ago by Guangchuang Yu800

What should I change below to make bitr work.

bitr(mytestgenes, fromType="ENSEMBLID", toType="ENTREZID", OrgDb="org.Hs.eg.db")
Error in bitr(mytestgenes, fromType = "ENSEMBLID", toType = "ENTREZID",  : 
  unused argument (OrgDb = "org.Hs.eg.db")
ADD REPLYlink written 15 months ago by saadmurtazakhan10

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

ADD REPLYlink written 15 months ago by Guangchuang Yu800
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