Multiple Testing


multtest : Resampling-based multiple hypothesis testing

limma : Linear Models for Microarray Data

 : GUI for limma package

SAM : Significance Analysis of Microarrays 

sma :  Statistics for Microarray Analysis

qvalue : for calculating q-values in multiple testing situations

HighProbability : estimates which genes have probabilities of differential expression at least as great as a specified threshold

Package Maintainer Title
affylmGUI Keith Satterley GUI for affy analysis using limma package
BeadExplorer Gareth Elvidge QC, normalisation, annotation and exploration of Illumina BeadChip data
bridge Raphael Gottardo Bayesian Robust Inference for Differential Gene Expression
copa James W. MacDonald Functions to perform cancer outlier profile analysis.
daMA Jobst Landgrebe Efficient design and analysis of factorial two-colour microarray data
DEDS Yuanyuan Xiao Differential Expression via Distance Summary for Microarray Data
diffGeneAnalysis Choudary Jagarlamudi Performs differential gene expression Analysis
EBarrays Deepayan Sarkar Empirical Bayes for Microarrays
edd Vince Carey expression density diagnostics
factDesign Denise Scholtens Factorial designed microarray experiment analysis
fdrame Effi Kenigsberg FDR adjustments of Microarray Experiments (FDR-AME)
GlobalAncova R. Meister Calculates a global test for differential gene expression between groups
globaltest Jelle Goeman Testing Association of Groups of Genes with a Clinical Variable
HEM HyungJun Cho Heterogeneous error model for identification of differentially expressed genes under multiple conditions
lapmix Yann Ruffieux Laplace Mixture Model in Microarray Experiments
limma Gordon Smyth Linear Models for Microarray Data
limmaGUI Keith Satterley GUI for limma package
LMGene Geun Cheol Lee LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
LPE Nitin Jain Methods for analyzing microarray data using Local Pooled Error (LPE) method
maanova Lei Wu Tools for analyzing Micro Array experiments
macat Joern Toedling MicroArray Chromosome Analysis Tool
maSigPro Ana Conesa Significant Gene Expression Profile Differeneces in Time Course Microarray Data
MergeMaid Xiaogang Zhong Merge Maid
metaArray Hyungwon Choi Integration of Microarray Data for Meta-analysis
multtest Katherine S. Pollard Resampling-based multiple hypothesis testing
nudge N. Dean Normal Uniform Differential Gene Expression detection
OCplus Alexander Ploner Operating characteristics plus sample size and local fdr for microarray experiments
OrderedList Claudio Lottaz Similarities of Ordered Gene Lists
pcot2 Sarah Song Principle Coordinates and Hotelling's T-Square method
pickgene Brian S. Yandell Adaptive Gene Picking for Microarray Expression Data Analysis
plgem Mattia Pelizzola Power Law Global Error Model
RankProd Fangxin Hong Rank Product method for identifying differentially expressed genes with application in meta-analysis
ROC Vince Carey utilities for ROC, with uarray focus
safe William T. Barry Significance Analysis of Function and Expression
SAGx Per Broberg Statistical Analysis of the GeneChip
siggenes Holger Schwender SAM and Efron's empirical Bayes approaches
sigPathway Weil Lai Pathway Analysis
simpleaffy Crispin Miller Very simple high level analysis of Affymetrix data
sscore Richard Kennedy S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
ssize Gregory R. Warnes Estimate Microarry Sample Size
twilight Stefanie Scheid Estimation of local false discovery rate
webbioc Colin A. Smith Bioconductor Web Interface