Hi I've been using the limma and eBayes function for looking at a set of affymetrix chips with 8 or so different groups within. Following the instructions on page 11=12 of the PDF guide, this works fine I think. My question regards different ways to specify the contrasts. If I wish to compare composite groups, e.g. (group1,group2) vs (group3,group4) and others is there a syntax to specify this within the makeContrasts function?, and where can I read about this?, or alternatively is there a better step at which I can achieve this (without changing my class vector repeatedly that is)? Stephen ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}

At 11:38 PM 20/01/2004, Stephen Henderson wrote: >Hi >I've been using the limma and eBayes function for looking at a set of >affymetrix chips with 8 or so different groups within. Following the >instructions on page 11=12 of the PDF guide, this works fine I think. > >My question regards different ways to specify the contrasts. If I wish to >compare composite groups, e.g. > >(group1,group2) vs (group3,group4) and others What about makeContrasts((group1+group2)/2-(group3+group4)/2,levels=design) ? Gordon >is there a syntax to specify this within the makeContrasts function?, and >where can I read about this?, or alternatively is there a better step at >which I can achieve this (without changing my class vector repeatedly that >is)? > >Stephen