GeneSelector-package: Stability and aggregation of ranked gene lists
In GeneSelector: Stability and Aggregation of ranked gene lists

Description Details Author(s)

The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various featured ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise.

Package:	GeneSelector
Type:	Package
Version:	1.5.1
Date:	2009-13-5
License:	GPL (version 2 or later)

Important steps of the workflow:

1.: Generate a Gene Ranking with RankingTstat, RankingFC, RankingWelchT, RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation
2.: Inspect the toplist using toplist.
3.: Prepare altered datasets using GenerateFoldMatrix or GenerateBootMatrix
4.: Get rankings for the altered datasets with RepeatRanking.
5.: Assess stability of rankings using GetStabilityOverlap, GetStabilityDistance, GetStabilityUnion.
6.: Aggregate different rankings with AggregateSimple, AggregatePenalty, AggregateMC or AggregateSVD.
7.: Inspect the similarity of methods visually using HeatmapRankings.
8.: Run the GeneSelector.