t.90th: Computes moderated gene wise t-statistics.

In GSEArot: GSEA rotation

Description

Computes gene wise t-statistic with variance stabilised by adding the 90th percentile.

Usage

t.90th(X, y = NULL)

Arguments

X	Gene expression matrix with samples as rows and genes as columns
y	Optional vector of 0/1 indicating sample phenotype

Details

Computes a gene wise t-statistic with variance stabilised by adding the 90th percentile of all the genes' standard deviations to a gene's standard devitation (Efron et al. 2001). If y is given, a two-sample test is performed, otherwise a one-sample test is performed. For a two-sample t-test the approach of Pan et al. (2003) is used.

Value

tS	Vector with one smoothed t-value for each gene

Author(s)

Guro D\orum

References

Efron, B., Tibshirani, R., Storey, J. D. and Tusher, V. (2001) Empirical Bayes analysis of a microarray experiment, J Amer Statist Assoc, 96, 1151-1160.

Pan,W., Lin,J. and Le,C.T. (2003) A mixture model approach to detecting differentially expressed genes with microarray data, Funct Integr Genomics, 3, 117<96>124.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--    or do  help(data=index)  for the standard data sets.

GSEArot documentation built on May 2, 2019, 4:56 p.m.