Monad transformers and PureScript's row-based effects are two complementary approaches to the problem of extensible effects.
Some effects in PureScript look a lot like the effects provided by certain monad transformers (StateT/ST/Ref, ExceptT/Exception, etc.), but there are differences in terms of how things compose. Take StateT and ExceptT for example: you can compose them in two ways, and get two different monad transformer stacks, with different behaviors (surrounding how state propagates when an exception occurs). There are valid use cases for each, but with the ST and Exception effects, there is only one way to combine them: the way the underlying (Javascript) runtimes chooses for us.
There are things which each one can do which the other cannot. Fortunately, we can mix and match in PureScript since we have the purescript-transformers library. A typical arrangement is to stick Eff on the bottom of a monad transformer stack.
_Edit_: of course, everything you can do with a monad transformer can be done more verbosely with pure functions and the underlying monad, so you _could_ replace monad transformers with Eff in many cases, but in practical terms, it might not be all that useable in some cases.