DESeq2 Normalization of time course

Question

[EVR]

Hi,

I am new to DESeq2 analysis. I have RNASeq raw count data from three different time points namely 0h, 5h, 1d. Every time point has triplicates for Control samples, Treatment-A, Treatment-B, Treatment-C. All I want to find is the differential expressed genes between Treated against Control samples(Treatment-A vs Control; Treatment-B vs Control; Treatment-C vs Control) within every time point. Now I would like to know whether , I should load raw counts of all the samples from all time points together into DESeq2 pipeline and compute diff. expression analysis OR load only the raw counts of particular time point(i.e. Control_0h, Treatment-A_0h, Treatment-B_0h and Treatment-C_0h) separately and perform differential gene expression analysis. Kindly guide me

Answer 1

[Carlo Yague]

In my opinion, it is best to load all the data because the estimation of the dispersion and of the variance-mean dependance will be more robust.

There is also this related post.