Report estimated p-values for each gene, from a SAM analysis
Report estimated p-values for each gene, from set of permutations in a SAM analysis
samr.pvalues.from.perms(tt, ttstar)
tt |
Vector of gene scores, returned by samr in component tt |
ttstar |
Matrix of gene scores (p by nperm) from nperm permutations. Returned by samr in component ttstar |
Jun Li and 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)
pv=samr.pvalues.from.perms(samr.obj$tt, samr.obj$ttstar)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.