Hello everyone, I am using DESeq2 for DEG analysis. I have a set of experiment which consists of 4 duplicates and it's not clear how to create the design object?

Here is my condition:

condition<- factor(c (group1 =rep ("treatment1",time=2), group2 = rep("treatment2",time=2), group3= rep("treatment3",time=2),group4 =rep("treatment4",time=2)))

.

 dds <- DESeqDataSetFromMatrix(countdata, coldata, design=~condition )

I think I should normalize within each group and compare the DE among groups.

Also, I’m a bit confused about what statistic method to apply with DESeq, contrast or interaction?

Thank you for help

Take a look at the vignette and the help page for ?results.

You can compare any groups using “contrast” in results and we have examples.