ebam(x, cl, method = z.ebam, delta = 0.9, which.a0 = NULL, control = ebamControl(), gene.names = dimnames(x)[[1]], ...)find.a0,
i.e.\ an object of class FindA0. Can also be a list (if method = chisq.ebam or
method = trend.ebam). For the latter case, see chisq.ebam.
If x is not a FindA0 object, then each row of x (or
exprs(x), respectively) must correspond to a variable (e.g., a gene or a SNP), and each column to
a sample.x is a FindA0 object.
Needs not to be specified if x is a list.
Typically, cl is specified by a vector of length ncol(x).
In the two class paired case, cl can also
be a matrix with ncol(x) rows and 2 columns. If x is
an ExpressionSet object, cl can also be a character string naming the column
of pData(x) that contains the class labels of the samples.
In the one-class case, cl should be a vector of 1's.
In the two class unpaired case, cl should be a vector containing 0's
(specifying the samples of, e.g., the control group) and 1's (specifying,
e.g., the case group).
In the two class paired case, cl can be either a numeric vector or a numeric matrix.
If it is a vector, then cl has to consist of the integers between -1 and
$-n/2$ (e.g., before treatment group) and between 1 and $n/2$ (e.g.,
after treatment group), where $n$ is the length of cl and $k$
is paired with $-k$, $k=1,\dots,n/2$. If cl is a matrix, one
column should contain -1's and 1's specifying, e.g., the before and the after
treatment samples, respectively, and the other column should contain integer
between 1 and $n/2$ specifying the $n/2$ pairs of observations.
In the multiclass case and if method = chisq.ebam or method = trend.ebam,
cl should be a vector containing integers between 1 and $g$, where $g$ is
the number of groups. In the two latter cases, cl needs not to be specified, if
x is a list. For details, see chisq.ebam.
For examples of how cl can be specified, see the manual of siggenes.method = z.ebam,
a modified t- or F-statistic, respectively, will be computed as proposed by Efron et al. (2001).
If method = wilc.ebam, a (standardized) Wilcoxon sum / signed rank statistic will
be used as expression score.
For an analysis of categorical data such as SNP data,
method can be set to chisq.ebam. In this case, Pearson's Chi-squared statistic
is computed for each row.
If the variables are ordinal and a trend test should be applied
(e.g., in the two-class case, the Cochran-Armitage trend test), method = trend.ebam
can be employed.
It is also possible to employ an user-written function for computing an user-specified
expression score. For details, see the vignette of siggenes.quan.a0 of find.a0. If
NULL, the suggested choice of find.a0 is used. Ignored if x is a matrix, data
frame or ExpressionSet object.ebamControl.nrow(x) specifying the names of the variables. By default,
the row names of the matrix / data frame comprised by x are used.method = z.ebam, see
z.ebam. If method = wilc.ebam, see wilc.ebam. If
method = chisq.ebam, see chisq.ebam.EBAM-class, find.a0, z.ebam,
wilc.ebam, chisq.ebam