cc00-2-significant-method: Generic Methods for Significance

In ClassComparison: Classes and Methods for "Class Comparison" Problems on Microarrays

Generic Methods for Significance

Description

In the world of multiple testing that is inhabited by most microarray or protein profiling experiments, analysts frequently perform separate statistical tests for each gene or protein in the experiment. Determining cutoffs that achieve statistical significance (in a meaningful way) is an inherent part of the procedure. It is then common to select the significant items for further processing or for preparing reports, or at least to count the number of significant items. These generic functions provide a standard set of tools for selecting and counting the significant items, which can be used with various statistical tests and various ways to account for multiple testing.

Usage

## S4 method for signature 'ANY'
cutoffSignificant(object, ...)
## S4 method for signature 'ANY'
selectSignificant(object, ...)
## S4 method for signature 'ANY'
countSignificant(object, ...)
## S4 method for signature 'ANY'
probDiff(object, p0, ...)

Arguments

object	an object that performs multiple statistical tests on microarray or proteomics data
p0	Prior probability that an observed value comes from the lnown distribution.
...	additional arguments affecting these generic methods

Value

cutoffSignificant returns appropriate cutoff values that achieve specified significance criteria.

selectSignificant returns a logical vector, with TRUE values indicating items that satisfy the cutoff making them statistically significant.

countSignificant returns an integer, representing the number of significant items.

Author(s)

Kevin R. Coombes [e-mail]

ClassComparison documentation built on Dec. 22, 2024, 3:01 p.m.