Hello, I am working on RNASEQ data with 4 treatments(Control, ABA, salt,sorbitol), 3 genotypes(col.0, lbd16-1, ds2.3) and three replicates. To test differently expressed genes of treated/untreated effect between lbd16 and col.0, I wrote my script like this:

dds <- DESeqDataSetFromMatrix(countdata, colData, design= ~ genotype + treatment + genotype:treatment)

dds$treatment <- relevel(dds$treatment , "Control")

dds$genotype <- relevel(dds$genotype , "Col.0")

keep <- rowSums(counts(dds)) >= 1 dds_F <- dds[keep,]

dds2 <- DESeq(dds_F)

dds2$group <- factor(paste0(dds2$genotype, dds2$treatment))

design(dds2) <- ~ group resultsNames(dds2)

It gives me an output :

[1] "Intercept" "genotypeds2.3vsCol.0" "genotypelbd16.1vsCol.0" [4] "treatmentABAvsControl" "treatmentNaClvsControl" "treatmentsorbitolvs_Control" [7] "genotypeds2.3.treatmentABA" "genotypelbd16.1.treatmentABA" "genotypeds2.3.treatmentNaCl" [10] "genotypelbd16.1.treatmentNaCl" "genotypeds2.3.treatmentsorbitol" "genotypelbd16.1.treatmentsorbitol".

My question is:

1. Is it the right script to find DEGs among treaments and genotypes?

2. will "res<-results(dds2, contrast=list( c("treatmentABAvsControl","genotypeds2.3.treatmentABA")))" give me the result that differently expressed genes of ABAvscontrol between ds2.3 and col.0. If not, what would be the right one?

3. If I just want to see DEGs of ABAvscontrol of Col0, is this right?

results(dds, contrast=c("treatment","ABA","Control"))

4.If I just want to see DEGs of ABAvs_control of lbd16, is this right?

results(dds, name="genotypelbd16.1.treatmentABA")