GeneSelector-package {GeneSelector} | R Documentation

## Excluding Genes from being candidates for differential expressions by combining various statistics and altered datasets.

### Description

The name 'Geneselector' stands for the exclusion of genes that might be considered differentially expressed. 'Selected' genes are those present at the top of the list in various featured ranking methods (currently 15). In addition, the stability of the findings are checked by creating perturbed versions of the original dataset, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise.

### Details

Package: | GeneSelector
Type: | Package
Version: | 0.9.5
Date: | 2008-31-1
License: | GPL (version 2 or later)

Most Important Steps for the workflow are:

1.
  Generate a Gene Ranking with RankingTstat, RankingFC, RankingWelchT, RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingBstat, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation, RankingGap
2.
  Inspect the toplist using `toplist`.
3.
  Prepare altered datasets using GenerateFoldMatrix or GenerateBootMatrix
4.
  Get rankings for the altered datasets with GetRepeatRanking.
5.
  Assess stability of rankings using GetStabilityLm, GetStabilityOverlap, RecoveryScore.
6.
  Aggregate different rankings with a bayesian approach with AggregateBayes or in a simple manner (AggregateSimple).
7.
  Inspect visually the similarity of methods using HeatmapMethods.
8.
  Combine everything into the GeneSelector.

### Author(s)

Martin Slawski martin.slawski@campus.lmu.de,
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix

Maintainer: Martin Slawski martin.slawski@campus.lmu.de.

[Package GeneSelector version 1.4.0 Index]