Description Usage Arguments Value Examples
This function implements Smyth's approach (empirical bayes estimate of error variance of genes, limma paper 2004).
1 | shrink.phi(phi.hat, den.df)
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phi.hat |
a numerical vector of the estimated of error variance of all genes. |
den.df |
denominator degree of freedom associated with the estimated variances phi.hat (=n sample -rank(design)). |
a list of 3 components
phi.shrink |
vector of shrinkaged estimates of variance. |
d0 |
estimated prior degree of freedom used inthe shrinkage procedure. |
phi0 |
estimated prior variance used in the shrinkage procedure. |
1 2 3 4 | phi.hat <- rchisq(1000, 1)
den.df <- 2
shrinkout <- rmRNAseq:::shrink.phi(phi.hat, den.df)
hist(shrinkout$phi.shrink)
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