Greetings, I have RNA-seq data need to be analyzed, How to do? I have two groups, one disease one no disease. Within each group, they received treatments of treatment A, B, C, D. This is all in one column in MetaData table (DiseaseTreatment), like NoDiseaseA, DiseaseA, NoDiseaseC, DiseaseC etc etc. How do I compared within DESEQ2 design? I want to compare NoDiseaseA-D to DiseaseA-C, and NoDisease overall to Disease overall.

dds <- DESeqDataSetFromMatrix(countData=mydata, colData=MetaData, design=~DiseaseTreatment)

then do: compare1 <- results(dds, contrast=c("DiseaseTreatment","NoDiseaseA", "DiseaseA"), independentFiltering=TRUE, alpha=0.05)

Is that right?

Many thanks.