samr (version 3.0)

samr.plot: Make Q-Q plot for SAM analysis

Description

Makes the Q-Q plot for a SAM analysis

Usage

samr.plot(samr.obj, del, min.foldchange=0)

Arguments

samr.obj

Object returned from call to samr

del

Value of delta to use. Delta is the vertical distance from the 45 degree line to the upper and lower parallel lines that define the SAM threshold rule.

min.foldchange

The minimum fold change desired; should be >1; default is zero, meaning no fold change criterion is applied

Details

Creates the Q-Q plot fro a SAm analysis, marking features (genes) that are significant, ie. lie outside a slab around teh 45 degreee line of width delta. A gene must also pass the min.foldchange criterion to be called significant, if this criterion is specified in the call.

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

# NOT RUN {
#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)


samr.plot(samr.obj, del=.3)
# }