EBSeq vs DESeq2 compare and contrast

[James Chappell]

Hello,

I am performing many DEG analyses lately, testing with both EBSeq & DESeq2, and EBseq gives more DE genes every time (given the same 10% FDR). I am always asked "so which one is better? or more trustworthy?" Is it correct that DESeq2 is more stringent, perhaps due to filtering more outliers & lowly expressed genes? What are the main factors that differentiate these these programs?

Apologies if you have answered this already.

Thanks,

James