RecoveryScore {GeneSelector} | R Documentation |
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.
RecoveryScore(RR, method = c("raw", "BH", "qvalue", "Bonferroni", "Holm", "Hochberg", "SidakSS", "SidakSD", "BY"), maxpval = 0.05)
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). |
A numeric vector of recovery scores for each perturbed dataset.
Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix
Pavlidis, P., Li, Q., Noble, W.S. (2003).
The effect of replication on gene expression microarray experiments.
Bioinformatics, 19, 1620-1627
GetStabilityLm, GetStabilityOverlap
### 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")