Hi all, If I have a 2x2 design (gen[AB], treat[CD]), I've created a design matrix so that I have 4 classes: A.C, A.D, B.C and B.D. Now I'm interested in finding the global differences between genA and genB, the global differences between treatC and treatD and their interaction, is it correct to specify contrasts like: (A.C + A.D) - (B.C + B.D) for genotypes (A.C + B.C) - (A.D + B.D) for treatments (A.C - A.D) - (B.C - B-D) for interactions (as in the manual) ? d ---------------------------------------------------------------------- ---- LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 03 06 80 153 info:www.5xmille at hsr.it - www.5xmille.org Disclaimer added by CodeTwo Exchange Rules 2007 http://www.codetwo.com

Hi Davide, On 8/11/2012 7:51 AM, Cittaro Davide wrote: > Hi all, > If I have a 2x2 design (gen[AB], treat[CD]), I've created a design matrix so that I have 4 classes: A.C, A.D, B.C and B.D. Now I'm interested in finding the global differences between genA and genB, the global differences between treatC and treatD and their interaction, is it correct to specify contrasts like: > > (A.C + A.D) - (B.C + B.D) for genotypes > (A.C + B.C) - (A.D + B.D) for treatments The above two are not really what you want. Instead you should divide each group by two, e.g.: (A.C + A.D)/2 - (B.C + B.D)/2 for genotypes Best, Jim > (A.C - A.D) - (B.C - B-D) for interactions (as in the manual) > > ? > > d > -------------------------------------------------------------------- ------ > LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO. > AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 03 06 80 153 > info:www.5xmille at hsr.it - www.5xmille.org > > Disclaimer added by CodeTwo Exchange Rules 2007 > http://www.codetwo.com > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099