RNAseq time series data w/ controls for each time point

[Mocca]

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

[dpryan]

You could use DESeq or edgeR still and just not do the pair-wise comparisons. Using DESeq syntax:

fit1 <- fitNbinomGLMs(cds, count~treatment*time)
fit0 <- fitNbinomGLMs(cds, count~time + treatment:time)
pvals <- nbinomGLMTest(fit1, fit0)

...assuming you're interested in genes that are differentially expressed by treatment when accounting for time point and a possible time-point:treatment interaction.

[Mocca]

Thanks for the reply.

I didn't consider doing it this way. Got a bit caught up in my control samples i guess. Will give it a try!

Cheers