RecoveryScore {GeneSelector}R Documentation

Stability measures for gene rankings

Description

Computes the Recovery Score of Pavlidis et al. (s. reference) below. The stability meausre is the proportion of genes that are declared significant (using usually multiple testing procedures) in both the original and the perturbed dataset.

Usage

RecoveryScore(RR, method = c("raw", "BH", "qvalue", "Bonferroni", "Holm", 
              "Hochberg", "SidakSS", "SidakSD", "BY"), maxpval = 0.05)

Arguments

RR An object of class RepeatRanking.
method The p-value adjustment method, s. AdjustPvalues. Can also be "raw"(default), then no adjustment will be done.
maxpval The maximum p-value at which a gene is still considered significantly differentially expressed (after adjustment).

Value

A numeric vector of recovery scores for each perturbed dataset.

Author(s)

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

References

Pavlidis, P., Li, Q., Noble, W.S. (2003).
The effect of replication on gene expression microarray experiments. Bioinformatics, 19, 1620-1627

See Also

GetStabilityLm, GetStabilityOverlap

Examples

### Load toy gene expression data
data(toydata)
### class labels
yy <- toydata[1,]
### gene expression
xx <- toydata[-1,]
### get ranking 
ordT <- RankingTstat(xx, yy, type="unpaired")
### Generate Leave-One-Out
loo <- GenerateFoldMatrix(xx, yy, k=1)
### Repeat Ranking with t-statistic
loor_ordT <- GetRepeatRanking(ordT, loo)
### Compute Recovery Score
rs_ordT <- RecoveryScore(loor_ordT, method="BH")

[Package GeneSelector version 1.4.0 Index]