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같은 질문에 다른 연구자들이 쓴 방법과, 그때 무엇이 문제였는지 보세요.
Choosing a method is usually framed as a question about what you can do, and it should be a question about what has worked. For most research questions there is a history: designs that were tried, the limitations their authors reported, and the modifications later papers made in response. That record is more useful than a methods textbook, because a textbook describes methods in general while the literature shows what happened when someone applied one to a question like yours. Reading the limitations sections of the three closest studies is often the single most efficient hour in designing a study.
Where should I start when choosing a method?
With the three studies closest to your question, and specifically their limitations sections. That is where the design problems are stated plainly.
What if the standard method has known problems?
Then say so and justify your choice against the alternative. A reviewer who knows the problem is reassured by seeing that you do too.
Is a novel method a stronger contribution?
Not usually, for a thesis. A well-executed standard design answers the question; a novel method adds a second thing to defend.