What does the 'coef' argument to topTable() actually do? I know it says in the manual: column number or column name specifying which coefficient or contrast of the linear model is of interest But what does that mean mathematically? Why does specifying the coefficient alter the results of the top table? Either a probe is differentially expressed or it isn't, right? I'm having trouble conceptualizing why there are multiple coefficients at this stage at all. Suppose my contrast is "MUvsWT=MU-WT". How do you get more than one result when you subtract WT from MU? If I run topTable(fit,coef=1) does that get me MU, WT, or MU-WT? If I run topTable(fit, coef=2) does that get me MU, WT, or MU-WT? If I run topTable(fit, coef=0) or topTable(fit, coef=2), I get an error. Which of those isn't a coefficient and why not? [[alternative HTML version deleted]]

Hi Ed, The 'coef' argument let user's specify the contrast for which toptable should be generated. So, if you made multiple contrasts like: contrast.matrix<-makeContrasts(Ten-Control,Eleven-Control,Twelve- Control, levels=design)## We made three contrasts here ten-control, eleven-control and twelve- control fit2<- contrasts.fit(fit,contrast.matrix) fit2 <- eBayes(fit2) Now if you want the toptable for first contrast in your matrix 'Ten-Control' specify coef=1, like this: topTable(fit2, coef = 1, adjust = "fdr", number = 50,sort.by='logFC') If you want toptable for 2nd contrast i.e. 'Eleven-Control' than specify coef=2, like this: topTable(fit2, coef = 2, adjust = "fdr", number = 50,sort.by='logFC') So, its just a way specifying your contrasts in numbers rather than writing whole contrast. The 'coef' count starts from 1 and not 0, therefore you get an error with 'coef=0'. Best Atul On 10-Jun-13 6:00 PM, Ed Siefker wrote: > What does the 'coef' argument to topTable() actually do? > I know it says in the manual: > > column number or column name specifying which coefficient or > contrast of the linear model is of interest > > But what does that mean mathematically? Why does specifying > the coefficient alter the results of the top table? Either a probe > is differentially expressed or it isn't, right? > > I'm having trouble conceptualizing why there are multiple coefficients > at this stage at all. Suppose my contrast is "MUvsWT=MU-WT". > How do you get more than one result when you subtract WT from MU? > > If I run topTable(fit,coef=1) does that get me MU, WT, or MU-WT? > If I run topTable(fit, coef=2) does that get me MU, WT, or MU-WT? > If I run topTable(fit, coef=0) or topTable(fit, coef=2), I get an error. > Which of those isn't a coefficient and why not? > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >