Dear all, I have faced with a problem in using clusterProfiler.
I have 152 differential expressed genes between cancer and normal tissues and I want to enrich their biological processes using clusterProfiler.
I was recommended to use enrichGO function and limit the background to the list of genes that have been expressed in both cancer and normal tissues. So I filtered genes with less than 10 counts and convert the ensembl IDs to gene symbol using biomaRt package. The same conversion was performed for 152 DEGs.
However when I run clusterProfiler I got the message than "no gene can be mapped" and that "it expected IDs like: TEKT3,MARF1,...".
I suspect to my inputs, so I compare the list of 152 DEGs with the list of backgrounds which consist of 12604 gene symbol. Strangely small number of DEGs were present in the background.
Is it possible that biomaRt had made mistake in ID conversion?
I will appreciate any recommendation