Hello all, I am using limma on Affymetrix data and I read and followed the User's Guide so far, ?but one thing is still not clear to me: Are the M-Values returned by the toptable- command estimated log2-fold changes? I know typing "?toptable" ?in R says "M: estimate of the effect or the contrast", but I don't understand what that means. If they aren't, where can I get fold changes for my data? I have 4 untreated and 4 treated experiments, my R code is: design<- cbind(c(1,1,1,1,1,1,1,1),c(0,0,0,0,1,1,1,1)) fit ? <- lm.series(exprs(Set),design) eb ? ?<- ebayes(fit) result <-toptable(coef=2,number=300,genelist=data,fit=fit,adjust="fdr") Thanks a lot for your help, Julia

At 06:33 PM 10/03/2004, Julia Engelmann wrote: >Hello all, > >I am using limma on Affymetrix data and I read and followed the User's Guide >so far, but one thing is still not clear to me: >Are the M-Values returned by the toptable- command estimated log2-fold >changes? The M-values are on the same scale as the expression values that you give lm.series(). If exprs(Set) contains log2-intensities, then coef=1 will contain log2-intensities for your first condition and coef=2 will contain log2-fold changes between your two conditions. If exprs(Set) contains loge-intensities then coef=2 is loge-fold changes. If exprs(Set) contains absolute intensities (not recommended) then coef=2 is the change is average value of the intensities. Gordon > I know typing "?toptable" in R says "M: estimate of the effect or >the contrast", but I don't understand what that means. >If they aren't, where can I get fold changes for my data? > >I have 4 untreated and 4 treated experiments, my R code is: >design<- cbind(c(1,1,1,1,1,1,1,1),c(0,0,0,0,1,1,1,1)) >fit <- lm.series(exprs(Set),design) >eb <- ebayes(fit) >result <-toptable(coef=2,number=300,genelist=data,fit=fit,adjust="fdr") > >Thanks a lot for your help, >Julia