| gt.multtest {globaltest} | R Documentation |
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.
gt.multtest(gt, proc = c("FDR", "FWER"))
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. |
This function is completely based on the
mt.rawp2adjp function from the
multtest package.
An object of class gt.result.
This function must be called prior to any selection of significant genes.
Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting
For references, type: citation("globaltest"). See also the vignette GlobalTest.pdf included with this package.
# Breast cancer data (ExpressionSet) from the Netherlands Cancer
# Institute with annotation:
data(vandeVijver)
data(annotation.vandeVijver)
gt <- globaltest(vandeVijver, "StGallen", annotation.vandeVijver)
sort(gt.multtest(gt))