samr.tail.strength {samr} | R Documentation |
Estimate tail strength for a dataset, from a SAM analysis
samr.tail.strength(samr.obj)
samr.obj |
Object returned by samr |
A list with components
ts |
Estimated tail strength. A number less than or equal to 1. Zero means all genes are null; 1 means all genes are differentially expressed. |
se.ts |
Estimated standard error of tail strength. |
Balasubrimanian Narasimhan and Robert Tibshirani
Taylor, J. and Tibshirani, R. (2005): A tail strength measure for assessing the overall significance in a dataset. Submitted.
#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=100) samr.tail.strength(samr.obj)