GeneSelector-package: Stability and aggregation of ranked gene lists
Description
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.Details
|
Package: |
| GeneSelector |
|
Type: |
| Package |
|
Version: |
| 1.5.1 |
|
Date: |
| 2009-13-5 |
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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.