I'm applying EBSeq-HMM on my time course read counts (4 time points). There are two possible normalization methods available in the package: "Median" and "Quantile".
This model clusters genes into their most likely path. What I see is that when I use Median normalization method on my data, Gene X's most likely path would be "Up-EE-Up" (EE stands for equally expressed). When I use Qunatile norm method, this gene's most likely path is "Up-Up-Up".
When I plotted the Median and Quantile normalized expression for this gene, I figured out that the slope of the gene expression between time point 2 and 3 in Median norm is less than Quantile. So probably that is why EBSeq-HMM didn't find the difference big enough to show an "Up" path for the genes. Now I don't know which norm method to trust or how to know which one is working better with EBSeq-HMM.
How I can I upload the photos?