tests/03-betamix.R

In NewmanOmics: Extending the Newman Studentized Range Statistic to Transcriptomics

library(NewmanOmics)

### pairedStat
data(LungPair)
lung <- as.matrix(log2(1 + LungPair))

set.seed(12345)
normal <- lung[, 1, drop=FALSE]
tumor  <- lung[, 2, drop=FALSE]
ps <- pairedStat(normal, tumor)
summary(ps@p.values)

fm <- fitMix3(as.vector(ps@p.values), print.level = 0)
### reduce displayed digits to avoid differences in NLM
### on different platforms
### FAILS anyway on M1Max and NoLD tests
## formatC(fm@mle, digits=3, format="e")
## round(fm@psi, 5)
## But the plots are indistinguishable.
plot(fm)