Variance Estimation of FMT Method (Fully Moderated T-Statistic)
Description
The FMT method computes posterior residual variances to be used in
the denominator of a moderated t-statistic from a linear model analysis of
gene expression data. It is an extension of the moderated t-statistic
originally proposed by Smyth (2004) .
LOESS local regression and empirical Bayesian method are used to estimate
gene specific prior degrees of freedom and prior variance based on average
gene intensity levels. The posterior residual variance in the denominator is
a weighted average of prior and residual variance and the weights are prior
degrees of freedom and residual variance degrees of freedom. The degrees of
freedom of the moderated t-statistic is simply the sum of prior and residual
variance degrees of freedom.