DEG analysis between distant species

[shuixiangyuer]

Hi all,

I am recently thinking about how to implement DEG analyses on two distant species. My idea is to get the expression values (like RPKM that corrected by GC and length bias), then use limma to call DEGs. The problem is, all DEGs might be confounded by evolutionary processes. I want to sort out those genes that significantly changed between species given that gene expression may fluctuate during evolution. One idea is to set a cutoff on their divergence, but I don't know what cutoff should be reasonable? Also, does anybody have other ideas?

Thanks,

Xuepeng