samr.missrate: Estimate the miss rate table for a SAM analysis

In bnaras/samr: SAM: Significance Analysis of Microarrays

Description

Estimates the miss rate table, showing the local false negative rate, for a SAM analysis

Usage

samr.missrate(samr.obj, del, delta.table, quant=NULL)

Arguments

samr.obj	Object returned from call to samr
del	Value of delta to define cutoff rule
delta.table	Object returned from call to samr.compute.delta.table
quant	Optional vector of quantiles to used in the miss rate calculation

Author(s)

Jun Li and Balasubrimanian Narasimhan and Robert Tibshirani

References

Tusher, V., Tibshirani, R. and Chu, G. (2001): Significance analysis of microarrays applied to the ionizing radiation response" PNAS 2001 98: 5116-5121, (Apr 24). http://www-stat.stanford.edu/~tibs/sam

Taylor, J., Tibshirani, R. and Efron. B. (2005). The “Miss rate” for the analysis of gene expression data. Biostatistics 2005 6(1):111-117.

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)

delta.table<-samr.compute.delta.table(samr.obj)
del<- 0.3
siggenes.table<- samr.compute.siggenes.table(samr.obj, del, data, delta.table)


samr.missrate(samr.obj, del, delta.table)

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