I used Salmon and edgeR. I have some DGE with pvalues very very very low so close to zero. Actually the same genes are differentially expressed with a pvalue small ~ 0.001 in cuffdiff but not close to zero, so I am just wondering why the significance values are so different. Like geneA has a pvalue 0.001 in cuffdiff and a very small pvalue close to zero in Salmon?
Is this weird ? or just because of the number of genes in the background between aligning to a genome and mapping to transcript?