Arguments
gg.fit
GaGa or MiGaGa fit (object of type gagafit, as returned by fitGG).
x
ExpressionSet, exprSet, data frame or matrix
containing the gene expression measurements used to fit the model.
groups
If x is of type ExpressionSet or
exprSet, groups should be the name of the column
in pData(x) with the groups that one wishes to compare. If
x is a matrix or a data frame, groups should be a
vector indicating to which group each column in x
corresponds to.
sel
Numeric vector with the indexes of the genes we want to
draw new samples for (defaults to all genes). If a logical vector is
indicated, it is converted to (1:nrow(x))[sel].
underpattern
Expression pattern assumed to be true (defaults to
last pattern in gg.fit$patterns). Posterior
means are computed under this pattern. For example, if only the null
pattern that all groups are equal and the full alternative that all
groups are different are considered, underpattern=1 returns
the posterior means under the assumption that groups are different
from each other (underpattern=0 returns the same mean for all
groups).