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?
Hi Lorena, thanks for your suggestions! If i were to use res as a pairwise comparison e.g. MutantTreatedNeonatal vs WTTreatedNeonatal, do we define xs="group"? like this?
I noticed that all the samplegroups stil appear in the degplot for above^ it perplexes me why so when res2 is only defined for a pairwise comparison.
if you use genes you don't have to use res. Actually it may confuse what you see. xs should be equal to the column of your colData to use. Probably, genotype if that is the one you are using for the function results.
degPlot will show all the groups, because it is taking all the samples always. If you want only some samples, then subset dds to those samples.