I'm trying to run the KEGG pathway analysis using "GAGE" and having trouble of running it because ID conversion isn't working for me.
First of all, I'm dealing with "cow" RNA-seq data.
Here's the R code I used...
kg.bta=kegg.gsets("bta") kegg.gs=kg.bta$kg.sets[kg.bta$sigmet.idx] kegg.gs.sym <- lapplykegg.gs,eg2sym) lapply(kegg.gs.sym[1:3],head)
and the results are...
$`bta00970 Aminoacyl-tRNA biosynthesis`  NA NA NA NA NA NA $`bta02010 ABC transporters`  NA NA NA NA NA NA $`bta03008 Ribosome biogenesis in eukaryotes`  NA NA NA NA NA NA
I guess the "eg2sym" only works for "human".
I know I could also convert IDs on my RNA-seq data to Entrez, but I experienced a loss of about 5000 genes after conversion. And I'm worrying the loss of genes might distort the results.
So, I wonder if I can use "eg2sym" on cow data, and if not, how I can do it.