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Question: Differential expression across time points
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gravatar for udp3f
5 months ago by
udp3f0
udp3f0 wrote:

Hi,

I have a study design with 2 biological replicates where I want to know the differentially expressed genes in each of these across different time points. 

sample state Days
A DIAGNOSIS 0
A RELAPSE1 100
A RELPASE2 300
B DIAGNOSIS 0
B RELAPSE1 200
B RELAPSE2 324
B RELAPSE3 480

I want to contrast state DIAGNOSIS to the other states for each sample. What should be my design? I have tried a couple of ways to do this, going through forums but could not arrive at a contrast for all states e.g. A_stateDiagnosis_vs_RELAPSE1, B_stateDiagnosis_vs_RELAPSE3 etc.

Please suggest.

 

 

ADD COMMENTlink modified 5 months ago by Michael Love20k • written 5 months ago by udp3f0
1
gravatar for Michael Love
5 months ago by
Michael Love20k
United States
Michael Love20k wrote:

You can't do it per sample because you don't have replicates for this analysis: you just have a single observation per sample per state. You can do ~sample + state, where you would control for sample difference, and test for differences between the states.

ADD COMMENTlink written 5 months ago by Michael Love20k
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