samr.assess.samplesize.plot: Make a plot of the results from samr.assess.samplesize

In samr: SAM: Significance Analysis of Microarrays

Description

Plots of the results from samr.assess.samplesize

Usage

samr.assess.samplesize.plot(samr.assess.samplesize.obj, logx=TRUE)

Arguments

samr.assess.samplesize.obj	Object returned from call to samr.assess.samplesize
logx	Should logs be used on the horizontal (\# of genes) axis? Default TRUE

Details

Plots results: FDR (or 1-power) and FNR (or 1-type 1 error) from samr.assess.samplesize

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

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)

log2=function(x){log(x)/log(2)}

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

# assess current sample size (20), assuming 1.5fold difference on the log base 2 scale

samr.assess.samplesize.obj<- samr.assess.samplesize(samr.obj, data, log2(1.5))

samr.assess.samplesize.plot(samr.assess.samplesize.obj)

Example output

Loading required package: impute
Loading required package: matrixStats
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NULL

samr documentation built on May 1, 2019, 7:49 p.m.