samr.compute.delta.table {samr}R Documentation

Compute delta table for SAM analysis

Description

Computes tables of thresholds, cutpoints and corresponding False Discovery rates for SAM (Significance analysis of microarrays) analysis

Usage


samr.compute.delta.table(samr.obj, min.foldchange=0, dels=NULL, nvals=50)

Arguments

samr.obj Object returned from call to samr
min.foldchange The minimum fold change desired; should be >1; default is zero, meaning no fold change criterion is applied
dels vector of delat valeus used. By default, 50 values are chosen in the relevant operating chnage for delta. Delta is vertical the distance from the 45 degree line to the upper and lower parallel lines that define the SAM threshold rule.
nvals Number of delta values used

Details

Returns a table of the FDR and upper and lower cutpoints for various values of delta, for a SAM analysis.

Author(s)

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

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=50)

delta.table<- samr.compute.delta.table(samr.obj)


[Package samr version 1.26 Index]