Hi I would like to respectfully request more examples of the creation of design matrices for complex (ie involving more than 3 samples) loop designs using two-colour microarrays in the limma documentation. Although section 20.5 does give an example, with 5 RNA samples, one of these is a pool which makes an obvious reference when creating the design matrix as it is a coefficent we are not interested in estimating. However, other loop designs may not contain such an obvious sample, and I am struggling to figure out a way to create a design matrix for my current design that allows all contrasts of interest. In fact, at present, I have to create one design matrix to get some of the contrasts and another to get the rest. Is this a valid approach? Many thanks Mick

>Date: Fri, 9 Dec 2005 11:21:49 -0000 >From: "michael watson \(IAH-C\)" <michael.watson at="" bbsrc.ac.uk=""> >Subject: [BioC] Limma and creating design matrices for complex loop > designs >To: <bioconductor at="" stat.math.ethz.ch=""> > >Hi > >I would like to respectfully request more examples of the creation of >design matrices for complex (ie involving more than 3 samples) loop >designs using two-colour microarrays in the limma documentation. > >Although section 20.5 does give an example, with 5 RNA samples, one of >these is a pool which makes an obvious reference when creating the >design matrix as it is a coefficent we are not interested in estimating. >However, other loop designs may not contain such an obvious sample, and >I am struggling to figure out a way to create a design matrix for my >current design that allows all contrasts of interest. In fact, at >present, I have to create one design matrix to get some of the contrasts >and another to get the rest. Is this a valid approach? Valid if both design matrices span the full treatment space, but never necessary. Gordon >Many thanks > >Mick