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Old 01-26-2018, 11:39 AM   #1
adroval
Junior Member
 
Location: montevideo

Join Date: Oct 2016
Posts: 1
Question DESEQ2 Desing formula time series experiments with sham controls.

Hi. I have a time series RNASEQ experiment with 2 controls and 3 treated samples for each time point.

sample time condition
A 1 control
B 1 control
C. 1 treated
D. 1 treated
E 1 treated
F 2 control
G 2 control
H 2 treated
I 2 treated
J 2 treated
K 3 control
L 3 control
M 3 treated
N 3 treated
O 3 treated

I want to obtain the Differential gene expression for each of the time points and between time points:
time_1_control_vs_treated, time_2_control_vs_treated, time_3_control_vs_treated.
time1_vs_time2
time2_vs_time3
time1_vs_time3


What should I include in the design formula?

Thank you
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deseq2, dge, expression, rnaseq, sequencing

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