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siggenes (version 1.46.0)

Multiple testing using SAM and Efron's empirical Bayes approaches

Description

Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

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Version

Version

1.46.0

License

LGPL (>= 2)

Maintainer

Holger Schwender

Last Published

February 15th, 2017

Functions in siggenes (1.46.0)

limma to SAM or EBAM

Number of cells in a histogram

HTML page for a SAM or an EBAM object

EBAM and SAM for Fuzzy Genotype Calls

Estimation of the prior probability

SAM Analysis of Linear Trend

Classes sumSAM and sumEBAM

Computation of the Fudge Factor

Rowwise Wilcoxon Rank Sum Statistics

Links for a list of genes

Help files or argument list for EBAM-specific methods

Empirical Bayes Analysis of Microarrays

EBAM analysis Using t- or F-test

Significance Analysis of Microarray

siggenes-internal

Internal siggenes functions

Help files or argument list for FindA0-specific methods

SAM Analysis Using Wilcoxon Rank Statistics

Finding the Threshold Delta

plotFindArguments

SAM Analysis Using a Modified t-statistic

EBAM Analysis for Categorical Data

EBAM Analysis Using Wilcoxon Rank Statistics

Density Estimation

List of the significant genes

Computation of the q-value

SAM Analysis for Categorical Data

EBAM Analysis of Linear Trend

Further EBAM Arguments

CSV file of a SAM or an EBAM object

Further SAM Arguments

Help files or argument list for SAM-specific methods

Links for a SAM or an EBAM object