I have two microarray data set considering differentiation in two cell lines. 8 time points for each experiment for the control and treatment, and no replicates (sad...).
Now I am trying to find the changed genes with maSigPro, which employes regression model. In one experiment I got 10,000 changed genes, while in the other experiment only less 100 changed genes.
It seems very unreasonable to get such results, I suspect that the lack of replicates may be a problem.
I would like to know your experience with time-course data, and any suggestion for the no-replicates analysis?