For all possible absolute log2 fold changes (LFC), which genes have at least this fold change at a specified False Discovery Rate?

limma_confects(fit, coef = NULL, fdr = 0.05, step = 0.01, trend = FALSE)

Arguments

fit

A limma MArrayLM object.

coef

Column number of coefficient or contrast to test.

fdr

False Discovery Rate to control for.

step

Granularity of log2 fold changes to test.

trend

Should treat(..., trend=TRUE) be used?

Value

See nest_confects for details of how to interpret the result.

Details

Results are presented in a table such that for any given LFC, if the reader chooses the genes with abs(confect) less than this they are assured that this set of genes has at least this LFC (with the specified FDR). The confect column may also be viewed as a confidence bound on the LFC of each gene, with a dynamic correction for multiple testing.

fit should be produced using lmFit, and optionally contrasts.fit if a contrast is needed. It is not necessary to use eBayes, this function calls eBayes itself.