Arguments
proc
A character string containing the name of the multiple
testing procedure for which adjusted $p$-values are to be
computed. This vector should include any of the following:
"Bonferroni", "Holm", "Hochberg",
"SidakSS", "SidakSD", "BH", "BY",
"maxT", "minP", "q".
X
A data frame or matrix, with $m$ rows corresponding to variables
(hypotheses) and
$n$ columns to observations. In the case of gene expression data, rows
correspond to genes and columns to mRNA samples. The data can
be read using read.table.
classlabel
A vector of integers corresponding to observation (column)
class labels. For $k$ classes, the labels must be integers
between 0 and $k-1$. For the blockf test option,
observations may be divided into
$n/k$ blocks of $k$ observations each. The observations are
ordered by block, and within each block, they are labeled using the
integers 0 to $k-1$.
test
A character string specifying the statistic to be
used to test the null hypothesis of no association between the
variables and the class labels.
If test="t", the tests are based on two-sample Welch t-statistics
(unequal variances).
If test="t.equalvar", the tests are based on two-sample
t-statistics with equal variance for the two samples. The
square of the t-statistic is equal to an F-statistic for $k=2$.
If test="wilcoxon", the tests are based on standardized rank sum Wilcoxon statistics.
If test="f", the tests are based on F-statistics.
If test="pairt", the tests are based on paired t-statistics. The
square of the paired t-statistic is equal to a block F-statistic for $k=2$.
If test="blockf", the tests are based on F-statistics which
adjust for block differences
(cf. two-way analysis of variance).
rawpcalc
A character string specifying how to calculate
nominal/raw p-values. The possible choices are "Parametric"
or "Permutation".
side
A character string specifying the type of rejection region.
If side="abs", two-tailed tests, the null hypothesis is rejected for large absolute values of the test statistic.
If side="upper", one-tailed tests, the null hypothesis is rejected for large values of the test statistic.
If side="lower", one-tailed tests, the null hypothesis is rejected for small values of the test statistic.
...
Further arguments for mt.maxT, mt.minP, qvalue.