Question: Genes not mapping to pathway!
1
gravatar for Parham
4.8 years ago by
Parham1.4k
Sweden
Parham1.4k wrote:

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

 

kegg pathview • 2.3k views
ADD COMMENTlink modified 4.8 years ago by Gian350 • written 4.8 years ago by Parham1.4k
2
gravatar for Gian
4.8 years ago by
Gian350
Canada
Gian350 wrote:

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.

ADD COMMENTlink written 4.8 years ago by Gian350

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

ADD REPLYlink written 4.8 years ago by Parham1.4k
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