qvalue package in R: Can it be used with very small proportion of true alternatives?
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6.2 years ago
ckhh • 0

Hi,

I'm trying to use 'qvalue' package in r to work out the true proportion of alternatives.

I get pi0 is >1 with small lambda.

pi0.lambda seems to decrease as lambda increases.

In my simulated dataset I have only a very small proportion of true alternatives. (approx 0.001%)

Can this be the reason?

Is there any way I can work out the true proportion of alternative test?

qvalue very small proportion of true alternatives • 1.4k views
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