Dear List,

I think this may be a simple question for you but I wanna make it sure for
further steps.
I have already done some of data pre-processing procedures for my affymetrix
yeast2 arrays. My next step is to get *ratios* from various conditions in wt
and mutant following by fold-change comparison. So my question is which step
I should scale my dataframe for comparison?

Here are parts of my codes (codes with underline are the questions):

wt.pt.f1 <- exprs(esetsub[, 1])- exprs(esetsub[, 17])
wt.pt.f2 <- exprs(esetsub[, 2])- exprs(esetsub[, 18])
wt.pt.f <- cbind(wt.pt.f1, wt.pt.f2)
wt.pt.f <- new("ExpressionSet", exprs= as.matrix(wt.pt.f))
*wt.pt.f <- scale(exprs(wt.pt.f))      ### not sure

*mut.pt.f1 <- exprs(esetsub[, 9])- exprs(esetsub[, 21])
mut.pt.f2 <- exprs(esetsub[, 10])- exprs(esetsub[, 22])
mut.pt.f <- cbind(mut.pt.f1, mut.pt.f2)
mut.pt.f <- new("ExpressionSet", exprs= as.matrix(mut.pt.f))
*mut.pt.f <- scale(exprs(mut.pt.f))    **### not sure*

gg      <- cbind(wt.pt.f, mut.pt.f)
*gg      <- scale(gg)*              *### not sure*
pt.f1   <- gg[,3]-gg[,1]
pt.f2   <- gg[,4]-gg[,2]
gg1     <- cbind(gg, pt.f1, pt.f2)
gg2     <- new("ExpressionSet", exprs=as.matrix(gg))
....... followed by further steps


As seen above, where should I scale the ratios? Scale wt and mut separately
or together before getting pt.f1 and pt.f2 ratios??
Many many thanks!!!!!

Hui-Yi

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