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Old 08-07-2013, 05:32 AM   #1
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Location: Oslo

Join Date: Mar 2012
Posts: 9
Post RNAseq time series data w/ controls for each time point

Hi everyone,

I am currently working on a RNAseq data set consisting of 4 time points where each time point has 6 challenged and 6 control individuals (not paired). I have used both DEseq and edgeR for pairwise comparisons such as: time 1 - challenged vs control which worked nicely.

I am not sure that the reported DE genes at one time point is comparable to the DE genes at another time point. Thus I am looking for a package that can handle time series data. I have found several but none of them handles controls on each time point but prefers a base line expression level or a time 0 (which I don't have).

I can manage with my pairwise analyses, but if any of you have good suggestions to what I might try I would appreciate it greatly!

Thanks in advance
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