Dear Bioconductor users and developers! We have a complex experiment (for me) and we would like to receive suggestions on how to analyse it, if possible. The design is: Var A Var B Var C Var D ------------- ------------- ------------- ------------- T1 T2 T1 T2 T1 T2 T1 T2 Vars A and C are resistant and Vars B and D are susceptible to T1. T2 is a controll. We are interested to get the data from Vars, treatments (T1 and T2) and their interactions effects I do an analysis using limma for each Vars, but, I dont have an ideia how I do an analyse for all. I appreciate any comentary and/or papers suggestions. The data set are in a matrix after normalization with vsn package. Thank you -- Marcelo Luiz de Laia Ph.D Student in Genetics and Plant Breeding S?o Paulo State University (http://www.unesp.br/eng/) School of Agricultural and Veterinary Sciences Department of Technology Via de Acesso Prof.Paulo Donato Castellane s/n 14884-900 Jaboticabal - SP - Brazil Fone: +55-016-3209-2675

This design is called a 2-way factorial. If these are 2 channel arrays with T1 and T2 on each array, this is called a split plot design, with Variety as the whole plot treatment. To do a proper analysis, you need to have replicates. There are many good books on the analysis of experiments which do not require lots of mathematics. The texts by Kuehl and by Montgomery are very popular, but almost any book on experimental design will have this information. --Naomi At 09:42 AM 1/23/2006, Marcelo Luiz de Laia wrote: >Dear Bioconductor users and developers! > >We have a complex experiment (for me) and we would like to receive >suggestions on how to analyse it, if possible. > >The design is: > > Var A Var B Var C Var D >------------- ------------- ------------- ------------- >T1 T2 T1 T2 T1 T2 T1 T2 > >Vars A and C are resistant and Vars B and D are susceptible to T1. T2 is >a controll. > >We are interested to get the data from Vars, treatments (T1 and T2) and >their interactions effects > >I do an analysis using limma for each Vars, but, I dont have an ideia >how I do an analyse for all. > >I appreciate any comentary and/or papers suggestions. > >The data set are in a matrix after normalization with vsn package. > >Thank you > >-- >Marcelo Luiz de Laia >Ph.D Student in Genetics and Plant Breeding >S?o Paulo State University (http://www.unesp.br/eng/) >School of Agricultural and Veterinary Sciences >Department of Technology >Via de Acesso Prof.Paulo Donato Castellane s/n >14884-900 Jaboticabal - SP - Brazil >Fone: +55-016-3209-2675 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor 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