Hi Folks I really like the package DEGreport and I hope to be able to utilize it However, I have a 3x2 matrix (each factor has 2 levels) with the following dds dds<-genotype,treatment, age, genotype:traetment, genotype:age, genotype:age:treatment. I factor in all of them to ~group with
dds$group <- factor(paste0(dds$genotype, dds$condition,dds$agegroup))
i wanted to use the function degPlot and the following is my command as
res=results(dds) degplot(dds = dds, res = res, n = 6, xs ="group")
Can i cross check if this is correct if i want to evaluate the top 6 genes across all my groups? It's not clear to me how i can select specific pairwisegroups like MutantTreatedNeonatal vs WTTreatedNeonatal
also does degsignature only compare 2 factors? as shown here- http://lpantano.github.io/DEGreport/articles/DEGreport.html#general-qc-figures-from-de-analysis is it possible that i can compare 3 variables based on my experimental design?