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 [[alternative HTML version deleted]]

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

On Wed, Oct 22, 2008 at 8:16 PM, Hui-Yi Chu <huiyi.chu at="" gmail.com=""> wrote: > Hi Sean, > > Yes, they are replicate in ratios. In other words, these ratios are from > untreatment and treatment of wt1, wt2, mut1,mut2, so total is 8 ratios as > below. > > untreatmen wt1, wt2, mut1, mut2 > treatment wt1, wt2, mut1, mut2 > > And I wanna get the second values like: > r1: untreatment mut1/wt1 > r2: untreatment mut2/wt2 > r3: treatment mut1/wt1 > r4: treatment mut2/wt2 > > Now we have 4 ratios. And then I will compare r3 vs r1, r4 vs r2 to get most > fold changes genes. (I know I need three replicates, but I cannot convince > my adviser, therefore, this is the strategy I can use so far. ) So the > question is should I scale the 8 ratios from wt and mut separately (twice) > or together(once) before I get the four values? Hi, Hui-Yi. You should not do any scaling. You can use the log fold changes directly. You seem to understand that this is not an optimal design, so I won't belabor that point. Sean > > On Wed, Oct 22, 2008 at 7:51 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> >> 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 > >