Estimate the miss rate table for a SAM analysis
Estimates the miss rate table, showing the local false negative rate, for a SAM analysis
samr.missrate(samr.obj, del, delta.table, quant=NULL)
samr.obj |
Object returned from call to samr |
del |
Value of delta to define cutoff rule |
delta.table |
Object returned from call to samr.compute.delta.table |
quant |
Optional vector of quantiles to used in the miss rate calculation |
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
Taylor, J., Tibshirani, R. and Efron. B. (2005). The “Miss rate” for the analysis of gene expression data. Biostatistics 2005 6(1):111-117.
#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)
delta.table<-samr.compute.delta.table(samr.obj)
del<- 0.3
siggenes.table<- samr.compute.siggenes.table(samr.obj, del, data, delta.table)
samr.missrate(samr.obj, del, delta.table)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.