Make a plot of the results from samr.assess.samplesize
Plots of the results from samr.assess.samplesize
samr.assess.samplesize.plot(samr.assess.samplesize.obj, logx=TRUE)
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 |
Plots results: FDR (or 1-power) and FNR (or 1-type 1 error) from samr.assess.samplesize
Jun Li and Balasubrimanian Narasimhan and Robert Tibshirani
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
#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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.