Genes not mapping to pathway!

Question

[Parham]

Hi, does anyone know any potential causes for following issue? I am following this workflow, and I don't get my genes mapped to any of the output pathways. Example is from one. Another thread I have going on here as well.

Error:

Getting gene ID data from KEGG...
Done with data retrieval!
[1] "Downloading xml files for spo03013, 1/1 pathways.."
[1] "Downloading png files for spo03013, 1/1 pathways.."
No of the genes or compounds mapped to the pathway!
Argument gene.idtype or cpd.idtype may be wrong.
Working in directory /home/parham/pombe/working_dir/gage03
Writing image file spo03013.deseq2.png

Answer 1

[5utr]

As the error says the gene.idtype you selected is different from the one you used as input. If you are using gene symbols you should specify gene.idtype="SYMBOL" inside the pathview() function.

[Parham]

Thanks Gian, I changed it to gene.idtype="KEGG" as I was advised and it worked. Thanks though!