GeneSelector-package      package:GeneSelector      R Documentation

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_D_e_s_c_r_i_p_t_i_o_n:

     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.

_D_e_t_a_i_l_s:


       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.

_A_u_t_h_o_r(_s):

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

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

