gt.multtest {globaltest}R Documentation

Correct globaltest results for multiple testing

Description

Corrects the raw p-values resulting from a call to globaltest for multiple testing, using either Benjamini and Hochberg's False Discovery Rate or Holm's procedure for controlling the Family-Wise Error Rate.

Usage

gt.multtest(gt, proc = c("FDR", "FWER"))

Arguments

gt The output of a call to globaltest.
proc The procedure to be used. Either "FDR" for Benjamini and Hochberg's (1995) False Discovery Rate-controlling procedure or "FWER" for Holm's (1979) Family-Wise Error Rate controlling procedure.

Details

This function is completely based on the mt.rawp2adjp function from the multtest package.

Value

An object of class gt.result.

Note

This function must be called prior to any selection of significant genes.

Author(s)

Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting

References

For references, type: citation("globaltest"). See also the vignette GlobalTest.pdf included with this package.

See Also

globaltest, gtGO.

Examples

    # Breast cancer data (exprSet) from the Netherlands Cancer
    # Institute with annotation:
    data(vandeVijver)
    data(annotation.vandeVijver)

    gt <- globaltest(vandeVijver, "StGallen", annotation.vandeVijver)
    sort(gt.multtest(gt))

[Package globaltest version 4.8.0 Index]