The refinement process

Along with the research methodology, the early part of your research will construct an outline plan for your investigation. For PhD, this almost always has at least two stages of primary research. The following notes are intended to apply for any of the possible research methodologies for your PhD - and even for other sorts of doctorate such as those involving performance.
Your carefully chosen literature review leads to the starting points for your investigation, and your research question suggests how the investigation will begin. But at this stage you should have no fixed ideas of how things will turn out - after all, if you already know the answer to your research question, then it is not research. So it is to be expected that following a first stage of your investigation, there will be a process of refinement of the research question and the direction of the investigation.
This refinement is the magically effective ingredient in modern inductive investigation, and was not fully taken into account in some of the founding writings on science (e.g. Whewell), not in the discussions of them by philosophers such as Rorty or Feyerabend. Some of them would regard such refinement as a kind of cheating, since for them it was crucial always to say in advance how evidence would be collected, examined, and evaluated. For them, if the researchers were to say: "we notice something really interesting here that will now be the focus of the rest of our research", they would be invalidating the whole project up to that point.
But to researchers, it is entirely legitimate to focus on what is new or surprising. For example if the initial results (surprisingly) bear out someone's ideas in a novel setting, then it seems entirely proper to explore the edges of the area where they seem to apply. If the initial results don't seem to match anyone's existing ideas, then further work is suggested to try to sketch out what ideas would fit better.
Rorty tells us not to cheat too much...