Hi all, I want to confirm that I am interpreting my results correctly. I am using DESeq2 to find differentially expressed genes and using the following code to extract results from the comparison between two treatments:

res<-results(dds2, contrast = c("Condition", "Control", "Treatment"))
resOrdered<- res[order(res$padj),]

write.csv(as.data.frame(resOrdered), file="savedfile.csv"

If I have gene A that has a log2foldchange of -2.0, that can be interpreted as "gene A was downregulated in the treatment group compared to the control", yes? I am concerned that I am not making the correct interpretations based on the order of my groups when I run the code. I can swap the position of "Control" and "Treatment," and gene A would then have a log2foldchange of +2.0, so I have assumed that whatever group I have on the right-hand side is the causative of up or downregulation comparatively. Thank you!

Your interpretation seems correct. You can always use plotCounts() or any custom plotting based on the normalized counts to confirm things like that.

Most people follow the convention of comparing to the control, so most people would do

res<-results(dds2, contrast = c("Condition", "Treatment", "Control"))

And say the Treated is upregulated compared to Control. But it's just a conventional preference.