[BioC] What is a good "control" for bacteria RNA-seq samples from a series of time points

[Simon Anders]

Hi Nancy

On 18/06/13 20:24, Yanxiang Shi wrote:
> Thank you for your reply! My only concern is my cells stopped growing /
> slow down after the treatment, so that the cell densities at certain time
> point are different between control and treated cells, while the time
> density at time points can be similar as Time zero. Thus I am worried some
> pathways that are controlled related to cell density will be transcribed
> differently. So should I have two controls: "a time zero no treatment" and
> "time point no treatment"?

How would this help? As the untreated cells will not slow down in their 
growth, the "untreated at time T" sample will be as badly matched for 
cell density as the "untreated at time 0" sample.

Or do you want to manually dilute the untreated time-course to mimic the 
density changes?

   Simon