Hello, Dears,

I may ask a quick question on the edger? 1. Does edger support continues variables as DESeq 2 does? 2. Do you think the number of differential expression genes from edger different from DESeq 2?

I just want to compare my result got from DESeq 2 with adger?

Thanks, Amare

1. edgeR supports completely general linear models, including continuous covariates and anything else you might think of. There is no restriction on the design matrix you give it. There is no special documentation about how to include continuous covariates in edgeR because it doesn't require any special action, you just proceed as you would for any linear model in R. Everything works as one would expect. The is an example of continuous covariates in the time course section of the limma User's Guide and the same code works for edgeR.

2. Who knows? It depends on which options you choose in both packages. My guess is that edgeR and DESeq2 might give similar numbers of DE genes if the edgeR likelihood ratio pipeline is used (glmLRT) but edgeR might be more conservative if you use the quasi-likelihood pipeline (glmQLFit), which is what we currently recommend.