Transmutation is the general ability to change something from one form, substance, element, etc. to another. It's easier to conceive of this power by breaking it down into two aspects: range and target. Range refers to the area of effect that the power can influence, or be used, while target is the subject which is affected. Atom Eve is great example of a user with a broader use and control of Transmutation as she can affect a fairly large area and multiple targets (herself, others, and even inanimate objects). It also differs from magical changes in that those caused by Transmutation are linked to scientifically definable mechanisms rather than to occult or supernatural ones.
Given the broad range of this power's application and target it if often sub-categorized to make it easier to define. Some examples are Elemental Control and Metamorphosis, which are both much more restricted uses of transmutation. Generally speaking, Elemental Control is typically restricted to external targets and has a relatively large range, while metamorphosis is usually restricted to the character's own body and thus has a very limited range and only one target.