Hello, I am running a glm analysis with edgeR on 64 biologically independent samples, with 3 factors. I have sex (M and F), age (P0, P7, P15, P30), and genotype (Control, Knock-Out). I have two separate questions, 1) How does genotype effect males and females differently (at each timepoint) 2) Within each genotype (i.e. males only) what are the differences between genotypes over time. I began with a csv file that provides relevant information for each sample and followed the User guide's suggestion of pasting each factor together to form groups.
>Genotype<-Samples$genotype >Stage<- Samples$stage >Sex<-Samples$sex >Group <- factor(paste(Genotype,Stage, Sex,sep="." ))
After this, I am not sure how to create my design matrix to ask the specific questions I am interested in?