Description Arguments Details Value Note Author(s)
average.pval.replicates
x |
a |
classes |
a |
Given a 2D table of pvalues, such as the detection pvalue
for each probe for each sample, compute an average
p-value for those samples which are replicates of each
other.
This uses the more correct calculation of
p*(1-ln(p)), where p = p1*p2
, which is easily
generalised to >2 replicates.
a matrix
or data.frame
of 'averaged'
p.values. See Details.
Since detection pvals=0.00000 are quite common, and log(0) == NaN, if any of the p-values are 0, then the averaged p-value is also set to 0. I'm not 100% sure this is the best approach – it's certainly correct of all values are 0, but theoretically, 1 sample could have P=1.0 and the other P=0.
Mark Cowley, Mark Pinese
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