Hi, I am using dyngen for some knockdown simulations. I have controlled the random seed for both the control experiments and the KD experiments. I also used KD mode with parameter = 1 to simulate the control. From the mRNA abundance change plots, the KD and control share the same trajectory before the knockdown. So here I think all the DEGs (by Wilcoxon test) I calculate using the mRNA abundance at the same simulation time window should reflect the true KD-induced DEGs.
However, I observed that some upstream nodes of the KD node can vary significantly. For example, in the regulation below:
A
/ \
B C ← KD
I can also observe significant changes in A and B. Is this a bug, or is it expected from the GSSA algorithm?
Hi, I am using dyngen for some knockdown simulations. I have controlled the random seed for both the control experiments and the KD experiments. I also used KD mode with parameter = 1 to simulate the control. From the mRNA abundance change plots, the KD and control share the same trajectory before the knockdown. So here I think all the DEGs (by Wilcoxon test) I calculate using the mRNA abundance at the same simulation time window should reflect the true KD-induced DEGs.
However, I observed that some upstream nodes of the KD node can vary significantly. For example, in the regulation below:
A
/ \
B C ← KD
I can also observe significant changes in A and B. Is this a bug, or is it expected from the GSSA algorithm?