The DESeq2 vignette, under session "Group-specific condition effects, individuals nested within groups", suggests to use a trick from edgeR and "add a column
ind.n which distinguishes the individuals nested within a group".
More specifically, to avoid modeling with
~ ind + grp*cnd, which raises a matrix rank issue, the vignette suggests to use
~ grp + grp:ind.n + grp:cnd, with
ind.n being the added column from above.
My question is whether
grp can be interpreted as the comparison between individuals within the different groups of
cnd is zero (or the reference value), as it would be the case for
~ ind + grp + cnd + grp:cnd.
Any help would be much appreciated.