Question: DESeq2 Normalization of time course
gravatar for EVR
3.9 years ago by
EVR570 wrote:


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

rna-seq deseq2 normalization • 1.7k views
ADD COMMENTlink modified 3.8 years ago by bioinfo1730 • written 3.9 years ago by EVR570
gravatar for Carlo Yague
3.9 years ago by
Carlo Yague5.0k
Carlo Yague5.0k wrote:

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.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Carlo Yague5.0k
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