BY {sgof}

Benjamini-Yekutieli (BY) multiple testing procedure

Description

Performs the Benjamini-Yekutieli FDR-controlling method for multiple hypothesis testing.

Usage

BY(u, alpha = 0.05)

Arguments

u

A (non-empty) numeric vector of p-values.

alpha

Numeric value. The significance level of the test.

Details

The function BY allows for the application of the Benjamini and Yekutieli (2001) false discovery rate controlling procedure under dependence assumptions. The false discovery rate is estimated by the simple method proposed by: Dalmasso, Broet, Moreau (2005), by taking n=1 in their formula.

Value

A list containing the following values:

Rejections

The number of effects declared by the BY procedure.

FDR

The estimated false discovery rate.

Adjusted.pvalues

The adjusted p-values.

data

The original p-values.

alpha

The specified significance level for the test.

call

The matched call.

Author(s)

Irene Castro Conde and Jacobo de Uña Álvarez

References

Benjamini Y and Yekutieli D (2001). The control of the false discovery rate in multiple testing under dependency. Annals of Statistics 29, 1165–1188.

Dalmasso C, Broet P and Moreau T (2005). A simple procedure for estimating the false discovery rate. Bioinformatics 21:660–668

See Also

plot.BY,summary.BY,BBSGoF

Examples

res<-BY(Hedenfalk$x)
summary(res)   #number of rejected nulls, estimated FDR
plot(res)   #adjusted p-values