Time Course Design in DESeq2

Question

[gkuffel22]

Hoping for some help. I can't seem to wrap my brain around how I should set up my design in DESeq2. Here are the details, I have 6 samples from each patients. I have two patients. Each sample represents a different timepoint of treatment. For each patient I have 2 age-matched healthy controls. So I have 8 samples that correspond to patient 1 and 8 samples that correspond to patient 2. We want to do two things:

1. Identify any DE miRNAs within a patient as a result of the treatment over time.
2. Identfify any DE miRNAs between patients at any of the time points.

I'm also really not sure of how to incoroporate the controls. Any help is greatly appreciated.

Answer 1

[shoujun.gu]

for 1: check maSigpro. for 2: any DE analysis package can do it.

[gkuffel22]

Thanks for the reply. Both 1 & 2 can be accomplished in DESeq2. I am looking for a DESeq2 expert to help me set up the design and interaction terms.

[shoujun.gu]

ok, i see. But all these information should be found in DESeq2 manual.

[gkuffel22]

I actually consider myself very well-versed with the DESeq2 manual and vignettes. Although there is a vignette that describes time course analysis using the Fission dataset I am having a difficult time relating it to my specific conditions. This is why I am reaching out to the community looking for a DESeq2 expert.

Answer 2

[gkuffel22]

Is it reasonable to use the design below to identify DEmiRNAs between patients?:

ddsHTSeq1 <-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design = ~ Time + Patient)