topTable.SE: Add a moderated SE column to a topTable object.

In drmjc/microarrays: A collection of microarray and genomic helper code.

Description

moderated SE's are fit$stdev.unscaled * sqrt(fit$s2.post) unmoderated SE's are fit$stdev.unscaled * fit$sigma from p53 & 54 limma userguide: for gene j, contrast k: ujk = fit$stdev.unscaled = unscaled stdev sj = fit$sigma = gene j's residual variance, with dj df Bjk = linear model estimates = the logFC's tstat.ord <- signal/SE <- Bjk/(ujk.sj) <- fit$coef/(fit$stdev.unscaled * fit$sigma) tstat.mod <- signal/SE' <- Bjk/(ujk.s'j) <- fit$coef/(fit$stdev.unscaled * sqrt(fit$s2.post)) ^^^^ which follows a t-dist with d0 + dj d.f. s2.post is the weighted avg of s2.prior and sigma^2 with weights proportional to df.prior and df.residual, respectively.

Usage

  topTable.SE(fit, coef = NULL, ...)

Arguments

fit	see topTable
coef	the coefficient index. if NULL, this is set to 1.
...	arguments passed to topTable

Value

a topTable object produced by topTable, in addition to an “SE” column containing the moderated standard errors.

Author(s)

Mark Cowley, 2010-11-12

drmjc/microarrays documentation built on May 15, 2019, 2:26 p.m.