I has just started using Deseq2 to discovery deferentially expressed genes (DEGs).
In my data, I have 6 strains (S2,S3,S4,S5,S6,S7), each of which was studied at 2 time points (T1,T2), under 2 conditions ( drought, water), and with 2 replicates.
I performed the analysis like this: 1) Upload counts data for all strains and all conditions (48 columns) to the deseq2 at once, performed comparison between "T1S2water" and "T1S2drought", and got 0 DEGs. 2) Upload counts data for T1S2water and T1S2drought (4 columns) to the deseq2, performed the same comparison, and got 4 DEGs. 3) Upload counts data for T1S2water, T1S2drought,T2S2water, and T2S2drought (8 columns), performed the comparison and got 23 DEGs.
I am wondered that Why the number of the columns uploaded to the Deseq2 affected the number of DEG. Note that the reported DEGs seem to involved in the drought response that I interested.
