We are performing a transcriptome analysis with DESeq2.
We have three factors: treatment (control and drought), climate (CO2 and ambient) and zone in the leaf (zone1, zone2, zone3).
For each possible combination, we have 3 biological replicates (no technical replicates). The PCA showed us that we have 2 outliers. They are not in the same group, so this leaves us with 2 biological replicates for two of our sample groups.
I've been looking on the internet for information on how many biological replicates I need at minimum using DESeq2. I did find some information ( https://assets.geneious.com/manual/10.2/GeneiousManualsu100.html ), but I want to be sure before continuing. Running DESeq2 does not prompt an error message. Removing the two outliers results in more significant genes.
Thank you for your advice and time.
Antwerp University - Belgium