Dear all,

please if I may ask a question that may have been asked before, it is  about basics of limma and edgeR :

sometimes in the documentation and in some examples, the design matrix is specified as :

1) design <- model.matrix(~group)

and, in some other examples, as :

2) design <- model.matrix(~0+group, data=y$samples)

please could you let me know your recommendations of design1 vs design2. Thank you ;) !

bogdan

Have you looked at Section 9.2 of the limma User's Guide? That explains the difference between these two design matrices in some detail. The section begins:

There are two different ways to form the design matrix. We can either

1. create a design matrix which includes a coefficient for the mutant vs wild type difference, or
2. create a design matrix which includes separate coefficients for wild type and mutant mice and then extract the difference as a contrast.