samr.compute.delta.table {samr}

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 delta values used. Delta is the vertical distance from the 45 degree line to the upper and lower parallel lines that define the SAM threshold rule. By default, for array data, 50 values are chosen in the relevant operating change for delta. For sequencing data, the maximum number of effective delta values are chosen automatically according to the data.

nvals

Number of delta values used. For array data, the default value is 50. For sequencing data, the value will be chosen automatically.

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)