adjPval: Generate FDR adjusted P values for F test result.
In maanova: Tools for analyzing Micro Array experiments

Description Usage Arguments Value Author(s) Examples

This function takes a result object from matest and calculate the FDR adjusted P values. The new P values will be appended to the input object as additional fields. It has four options; "stepup" (Hochberg and Benjamini, 1990), "adaptive" (Benjamini and Hochberg, 2000), "stepdown" (Westfall and Young, 1993) and "jsFDR" (Storey, 2002). "jsFDR" option uses 'qvalue' package by John Storey and user suppose to install 'qvalue' package before using this option. There is no default option, thus you need to specify one option.

1	adjPval(matestobj, method=c("stepup","adaptive", "stepdown", "jsFDR"))

`matestobj`	An object of class `matest`, which is the result from `matest`.
`method`	The method for FDR control.

An object of class matest with the following fields added for each F test:

`adjPtab`	FDR adjusted tabulated P values.
`adjPvalperm`	FDR adjusted permutation P values.

Hao Wu

data(abf1)
## Not run:  
fit.full.simple = fitmaanova(abf1,formula = ~Strain)
# F-test strain effect
ftest.all = matest(abf1, fit.full.simple, term="Strain",n.perm= 1000)
# make FDR adjusted P values
ftest.all = adjPval(ftest.all, 'jsFDR')
# there will be new fields in test.strain.fix after this

## End(Not run)

Attaching package: 'maanova'

The following object is masked from 'package:base':

    norm

Warning message:
In any(parsed.formula$random) :
  coercing argument of type 'double' to logical
Doing F-test on observed data ...
Doing permutation. This may take a long time ... 
Finish permutation #  100 
Finish permutation #  200 
Finish permutation #  300 
Finish permutation #  400 
Finish permutation #  500 
Finish permutation #  600 
Finish permutation #  700 
Finish permutation #  800 
Finish permutation #  900 
Finish permutation #  1000 
There were 50 or more warnings (use warnings() to see the first 50)