Hello! I am working with a single series time course data set looking at gene expression over a time series.

My design is as follows
Time Replicates Group uncut1i 0 1 1 uncut2i 0 2 1 uncut3i 0 3 1 uncut3ii 0 3 1 hab001 0 1 1 hab002 0 2 1 hab003 0 3 1 hab011 1 1 1 hab012 1 2 1 hab013 1 3 1 hab031 3 1 1 hab032 3 2 1 hab033 3 3 1 hab061 6 1 1 hab062 6 2 1 hab063 6 3 1 hab121 12 1 1 hab122 12 2 1 hab123 12 3 1 hab241i 24 1 1 hab242i 24 2 1 hab243i 24 3 1 hab243ii 24 3 1 hab481i 48 1 1 hab482i 48 2 1 hab483i 48 3 1 hab483_ii 48 3 1

I understand that I should only have one group because I am not comparing different experimental conditions, but rather how gene expression changes under one condition. I am having difficulty figuring out how to visualize the genes of interest determined by the masigpro algorithm. I get a list of genes and I can plot how specific genes change over time,but the plot is difficult to interpret. Is there a way to use PlotProfiles to group the replicates from each time point to show the general trend?

Here is my command for plot profiles PlotProfiles(ML005354a,cond=Time,repvect=Replicates,cex.xaxis = .7)

I now have an expression profile of an organ at various developmental time periods, such as 3 replicates in the first week, 5 replicates in the second week, 4 replicates in the third week, and 5 replicates in the fourth week, without any experimental controls. How can I use masigpro to make an experimental design.