{
data(stemHypoxia)
##Just to make a balanced dataset in the Fisher sense (2 samples per
## time*oxygen levels)
design<-design[design$time %in% c(0.5,1,5) & design$oxygen %in% c(1,5,21), ]
design$time<-as.factor(design$time)
design$oxygen<-as.factor(design$oxygen)
rownames(M)<-M[, 1]
#Keeping appropriate samples only
M<-M[, colnames(M) %in% design$samplename]
##ANOVA decomposition
fit<-lmdme(model=~time+oxygen+time:oxygen, data=M, design=design)
##ASCA for all the available terms, on those subjects/genes where at least
##one interaction coefficient is statistically different from zero (F-test
##on the coefficients).
id<-F.p.values(fit, term="time:oxygen")<0.001
decomposition(fit, decomposition="pca", scale="row", subset=id)
## Not run:
# loadingplot(fit, term.x="time", term.y="oxygen")
#
# ##Or change the axis order
# loadingplot(fit, term.x="oxygen", term.y="time")
#
# ##Or change the PC to display
# loadingplot(fit, term.x="time", term.y="oxygen", pc=2)
#
# ##Or the order of x-levels
# loadingplot(fit, term.x="time", term.y="oxygen", ord.x=3:1)
# ## End(Not run)
}
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