ebam.z:"numeric" representing the
expression scores of the genes.posterior:"numeric" representing
the posterior probabilities of the genes.p0:"numeric" specifying the
prior probability that a gene is not differentially expressed.local:"numeric" consisting of the
local FDR estimates for the genes.mat.fdr:"matrix" containing general
statistics such as the number of differentially expressed genes and
the estimated FDR for the specified values of delta.a0:"numeric" specifying the used
value of the fudge factor. If not computed, a0 will be
set to numeric(0).mat.samp:"matrix" containing
the permuted group labels used in the estimation of the null
distribution. Each row represents one permutation, each column
one observation (pair). If no permutation procedure has been used,
mat.samp will be set to matrix(numeric(0)).vec.pos:"numeric" consisting of
the number of positive permuted test scores that are absolutely
larger than the test score of a particular gene for each gene.
If not computed vec.pos is set to numeric(0).vec.neg:"numeric" consisting of
the number of negative permuted test scores that are absolutely
larger than the test score of a particular gene for each gene.
If not computed vec.neg is set to numeric(0).msg:"character" containing information
about, e.g., the type of analysis. msg is printed when the functions
print and summary are called.chip:"character" naming the microarray
used in the analysis. If no information about the chip is available,
chip will be set to "".signature(object = "EBAM"): Generates a plot of the
posterior probabilities of the genes for a specified value of
$Delta$. For details, see help.ebam(plot). For
the arguments, see args.ebam(plot).signature(object = "EBAM"): Prints general information
such as the number of differentially expressed genes and the estimated
FDR for several values of $Delta$. For details, see
help.ebam(print). Arguments can be listed by args.ebam(print).signature(object = "EBAM"): Shows the output of an
EBAM analysis.signature(object = "EBAM"): Summarizes the results
of an EBAM analysis for a specified value of $Delta$.
For details, see help.ebam(summary). For the arguments,
see args.ebam(summary).ebam, find.a0, FindA0-class