logic.bagging or logicFS
by an Empirical Bayes Analysis of Microarrays (EBAM). Only available for the classification
and the logistic regression approach of logic regression.
vim.ebam(object, data = NULL, cl = NULL, storeEBAM = FALSE, ...)logicFS or the output of an application of
logic.bagging with importance = TRUE.logic.bagging
or logicFS, and each row corresponds to an observation. Must be specified if
object is an object of class logicFS, or cl is specified. If
object is an object of class logicBagg and neither data nor cl
is specified, data and cl stored in object is used to compute the
ChiSquare statistics. It is, however, highly recommended to use new data to test
the interactions contained in object, as they have been found using the data
stored in object, and it is very likely that most of them will show up as interesting
if they are tested on the same data set.data.
Must be specified either if object is an object of class logicFS, or if data
is specified.vim.ebam.ebam and cat.ebam. For details, see the help files
of these functions from the package siggenes.logicFS containing
object is the output of logicFS or vim.logicFS
with addInfo = TRUE),delta used in the EBAM analysis (see help files for ebam);
by default: 0.9,EBAM (only available if storeEBAM = TRUE).logic.bagging or logicFS, the posterior probability
that this interaction is significant is computed using the Empirical Bayes Analysis of Microarrays (EBAM).
These posterior probabilities are used as the EBAM based importances of the interactions.
The test statistic underlying this EBAM analysis is Pearson's ChiSquare statistic. Currently,
the value of this statistic is computed without continuity correction.
Contrary to vim.logicFS (and vim.norm and vim.signperm),
vim.ebam does neither take the logic regression models into acount nor uses the out-of-bag
observations for computing the importances of the identified interactions. It "just" tests each
of the found interactions on the whole data set by calculating Pearson's ChiSquare statistic for
each of these interactions and performing an EBAM analysis. It is, therefore, highly recommended
to use an independent data set for specifying the importances of these interactions with vim.ebam.
logic.bagging, logicFS,
vim.logicFS, vim.norm, vim.chisq