I have some data from a Microarray experiment for 70 samples and they are for 3 different treatments across 5 timepoints (1h/2h/8h/24h/48h). This is how my data looks like; the number of samples I have for each Treatment for each time point.
I want to be able to compare upregulation and downregulation of genes between the 4 treatment groups at different time points.
In such a case, should I first create 2 columns in my metadata called Timepoint and Treatment Type first?
And how would I then create the design and contrast matrix? I appreciate any advice on this, thanks!