samr.tail.strength: Estimate tail strength for a dataset, from a SAM analysis

In bnaras/samr: SAM: Significance Analysis of Microarrays

Description

Estimate tail strength for a dataset, from a SAM analysis

Usage

samr.tail.strength(samr.obj)

Arguments

samr.obj

Object returned by samr

Value

A list with components

ts	Estimated tail strength. A number less than or equal to 1. Zero means all genes are null; 1 means all genes are differentially expressed.

,

se.ts

Estimated standard error of tail strength.

Author(s)

Jun Li and Balasubrimanian Narasimhan and Robert Tibshirani

References

Taylor, J. and Tibshirani, R. (2005): A tail strength measure for assessing the overall significance in a dataset. Submitted.

Examples

#generate some example data
set.seed(100)
x<-matrix(rnorm(1000*20),ncol=20)
dd<-sample(1:1000,size=100)

u<-matrix(2*rnorm(100),ncol=10,nrow=100)
x[dd,11:20]<-x[dd,11:20]+u

y<-c(rep(1,10),rep(2,10))

data=list(x=x,y=y, geneid=as.character(1:nrow(x)),
genenames=paste("g",as.character(1:nrow(x)),sep=""), logged2=TRUE)

samr.obj<-samr(data,  resp.type="Two class unpaired", nperms=100)

samr.tail.strength(samr.obj)

bnaras/samr documentation built on May 12, 2019, 11:27 p.m.