Although I relevel in the following way, the GRanges with results still lists BB as the negative log2FoldChange, wondering what I am doing incorrectly here? Thanks.

dds<-DESeqDataSet(se, design= ~batch + treatment)

dds$group <- factor(paste0(dds$treatment))

dds$treatment<-relevel(dds$treatment, ref="vehicle")

table(sampleTreatment)

design(dds) <- ~batch + group

dds <- dds[ rowSums(counts(dds)) > "1", ]

dds <- DESeq(dds, betaPrior = FALSE, fitType = c("local"))

# pairwise male vs female

BN_treatment_pw<-results(dds, format = c("GRanges"), contrast=c("group", "vehicle", "BB"))

BN_treatment_pw_padj.001 <- subset(BN_treatment_pw, padj<.001)

BN_treatment_pw_padj.001_sorted = BN_treatment_pw_padj.001[order(BN_treatment_pw_padj.001$padj), ]

BN_treatment_pw_padj.001_sorted

What do you want to be the denominator of the contrast? Can you look over the description of the ‘contrast’ argument in ?results