At 08:00 PM 20/10/2005, bioconductor-request at stat.math.ethz.ch wrote: >Date: Wed, 19 Oct 2005 14:26:42 -0400 >From: Naomi Altman <naomi at="" stat.psu.edu=""> >Subject: [BioC] ANCOVA in limma >To: bioconductor at stat.math.ethz.ch > >We would like to adjust our ANOVA-type analysis by using the >covariate "age". Because limma is based on contrast, rather than >"type III SS", it seems to me that the only way to proceed with an >ANCOVA-type analysis is to orthogonalize the design matrix against >the covariate. Is there a more straight-forward method? I think that the limma approach is essentially equivalent to SAS Type III Anova. I think you should get the same results from orthogonalizing your design matrix as you'd get from the standard limma analysis, in which you include age in the design matrix but not in your contrasts. If you find this isn't the case, let me know. Gordon >Naomi S. Altman 814-865-3791 (voice) >Associate Professor >Dept. of Statistics 814-863-7114 (fax) >Penn State University 814-865-1348 (Statistics) >University Park, PA 16802-2111