I'm using DESeq2 to analyse some RNA-seq data. I have different treatments (XXX, YYY and ZZZ) at different time points (2h, 4h, 8h), with DMSO used as a control for the treatment. 'se' is my SummarizedExperiment object containing the raw counts.
## create DESeqDataSet dds <- DESeqDataSet(se, design = ~ treatment + time + treatment:time) # make sure DMSO is the base level of the treatment factor dds$treatment <- relevel(dds$treatment, "DMSO") ## differential expression analysis dds<- DESeq(dds) ## get results # let's check the effect of treatment XXX res <- results(dds, contrast=c("treatment", "XXX", "DMSO")) ## MA plot plotMA(res)
Now, this is what my MA plot looks like:
Does this look right? It almost looks like the fold changes have not been shrunken! Is that the case?
Am I doing something wrong?