I have acquired data of pathogen inoculated susceptible and resistant cell-lines along with their controls (mock inoculated) at each time point. I have time points of 2 hr, 4hr, 8 hrs, 16 hr. I request you to let me know how to group the data.
I have tried following approach, please let me know whether I am correct or not?
First I have made a folder control and infected, within these folder I have made a subfolder of 2 hrs, 4hr, 8hr and 12 hr.
yashwant,
It depends on what you want in some ways. Really the main thing here is if you use the density grouping method with the minFrac at 50% you will lose some peaks. I would think that setting up the groups by time points would be fine. I have in the past also just put everything into class folders and then separated everything out afterwards. This way I have the t-test for the classes. It can be helpful to tell me if something didn't change particularly through time but rather just between classes.
Just reread your question. :) If I remember correctly you're going to have some problems with retention time alignment if you use subfolders.
Does that all make sense. Let me know how you get on.
Cheers,
Paul