Dermot, The limma users guide has really been expanded over the years and contains an excellent example of just what you need. In R, do: library(limma) limmaUsersGuide() then go to page 45 of the guide and read the whole section. I use the treatment-contrast parameterization presented on page 47. Good luck, Mark --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** Dermot Morris wrote: > Hi Mark, > > > > I came across a message you posed in the Bioconductor archives > requesting info on 2 x2 factorial designs in limma. > > I am trying to use limma in a 2x2 factorial using proteomic data also. > Have you come up with a satisfactory design in limma. I would be > interested in > > Using design matrix or similar for my work. > > > > Regards, Dermot > > > > Dr. Dermot Morris, > > Principal Research Officer, > > Teagasc, > > Animal Production Research Centre, > > Mellows Campus, > > Athenry, > > Co. Galway, > > Ireland. > > TEL: +353 91 845839 > > FAX :+353 91 845847 > > CEL :+353 87 2206113 > > email: dermot.morris at teagasc.ie <mailto:dermot.morris at="" teagasc.ie=""> > > >