How do you identify the genes which are differentially expressed using the
mb.long function? More specifically, in the fruitfly example (see below),
we begin with an expression matrix containing 2000 genes. How do I obtain
not only the proportion of differentially expressed genes, but also the
subset of genes which are differentially expressed?
data(fruitfly)
colnames(fruitfly) ## check if arrays are arranged in the default order
gnames <- rownames(fruitfly)
assay <- rep(c("A", "B", "C"), each = 12)
time.grp <- rep(c(1:12), 3)
size <- rep(3, nrow(fruitfly))
out1 <- mb.long(fruitfly, times=12, reps=size, rep.grp = assay, time.grp =
time.grp)
summary(out1)
plotProfile(out1, type="b", gnames=gnames, legloc=c(2,15),
pch=c("A","B","C"), xlab="Hour")
> summary(out1)
Length Class Mode
M 72000 -none- numeric
prop 1 -none- numeric
nu 1 -none- numeric
Lambda1 121 -none- numeric
percent 2 -none- numeric
size 2000 -none- numeric
con.group 36 -none- numeric
rep.group 36 -none- numeric
time.group 36 -none- numeric
HotellingT2 2000 -none- numeric
pos.HotellingT2 2000 -none- numeric
Thanks to anyone who can shed light on this matter.
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