[BioC] scale questions

[Sean Davis]

On Wed, Oct 22, 2008 at 5:39 PM, Hui-Yi Chu <huiyi.chu at gmail.com> wrote:
> 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!!!!!

I may be misunderstanding, but why do you want to scale the log
ratios?  Generally, you would not scale them at all.  And I really
cannot tell why you are forming ratios in the first place?  Do you
have replicates of any kind?

Sean