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))