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In stage 1 we test many SNPs, in stage 2 we try to confirm these SNPs. Usually we start with less sample, but then it's hard to detect a signal. For example, if we can afford 3000 samples, how to allocate these 3000 people in two stages?

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All I can say right now is that you're probably going to need some sort of pilot study. Could you describe your independent and dependent variables and what "confirming" is? –  Thomas Levine Jun 16 '11 at 2:01
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