Hi all, I have an experimental design for a Affy experiment that looks like this: Phen Line Sex Biol.Rep. File1 H 1 M 1 File2 H 1 M 2 File3 H 1 F 1 File4 H 1 F 2 File5 H 2 M 1 File6 H 2 M 2 File7 H 2 F 1 File8 H 2 F 2 File9 L 3 M 1 File10 L 3 M 2 File11 L 3 F 1 File12 L 3 F 2 File13 L 4 M 1 File14 L 4 M 2 File15 L 4 F 1 File16 L 4 F 2 This appears to be a slightly more complicated situation than the one proposed in the section 8.7 of the limma users guide (p.45) or by Jenny on this post: https://stat.ethz.ch/pipermail/bioconductor/2006-February/011965.html In particular, I am intersted in - Effect of "sex" (M vs F) - Interaction between "sex" and "phenotype ("line" nested) - Effect of "phenotype" in males - Effect of "phenotype" in females Line should be nested in phenotype, because they are random "strains" that happened to end up in phenotype H or L. Can I design this in limma? Is there a source of information about how to handle with this? In particular, can I design a single model matrix and then choose the contrasts I am interested in? Any help is much appreciated, paolo -- Paolo Innocenti Department of Animal Ecology, EBC Uppsala University Norbyv?gen 18D 75236 Uppsala, Sweden

You can design this in limma quite readily. Nesting really just means that only a subset of the possible contrasts are of interest. Just create the appropriate contrast matrix and you are all set. --Naomi At 12:08 PM 2/16/2009, Paolo Innocenti wrote: >Hi all, > >I have an experimental design for a Affy experiment that looks like this: > > Phen Line Sex Biol.Rep. >File1 H 1 M 1 >File2 H 1 M 2 >File3 H 1 F 1 >File4 H 1 F 2 >File5 H 2 M 1 >File6 H 2 M 2 >File7 H 2 F 1 >File8 H 2 F 2 >File9 L 3 M 1 >File10 L 3 M 2 >File11 L 3 F 1 >File12 L 3 F 2 >File13 L 4 M 1 >File14 L 4 M 2 >File15 L 4 F 1 >File16 L 4 F 2 > > >This appears to be a slightly more complicated >situation than the one proposed in the section >8.7 of the limma users guide (p.45) or by Jenny on this post: > >https://stat.ethz.ch/pipermail/bioconductor/2006-February/011965.html > >In particular, I am intersted in >- Effect of "sex" (M vs F) >- Interaction between "sex" and "phenotype ("line" nested) >- Effect of "phenotype" in males >- Effect of "phenotype" in females > >Line should be nested in phenotype, because they >are random "strains" that happened to end up in phenotype H or L. > >Can I design this in limma? Is there a source of >information about how to handle with this? In >particular, can I design a single model matrix >and then choose the contrasts I am interested in? > >Any help is much appreciated, >paolo > > >-- >Paolo Innocenti >Department of Animal Ecology, EBC >Uppsala University >Norbyv?gen 18D >75236 Uppsala, Sweden > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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