Hi,
I am currently analyzing time series data from plant tissues infected by a "compatible" and "incompatible" strain. A would like make sure to have the right design :
> coldata
condition time
C0_1 Comp 0
C0_2 Comp 0
C0_3 Comp 0
C6_1 Comp 6
C6_2 Comp 6
C6_3 Comp 6
C12_1 Comp 12
C12_2 Comp 12
C12_3 Comp 12
C18_1 Comp 18
C18_2 Comp 18
C18_3 Comp 18
C24_1 Comp 24
C24_2 Comp 24
C24_3 Comp 24
C30_1 Comp 30
C30_2 Comp 30
C30_3 Comp 30
C36_1 Comp 36
C36_2 Comp 36
C36_3 Comp 36
C42_1 Comp 42
C42_2 Comp 42
C42_3 Comp 42
C48_1 Comp 48
C48_2 Comp 48
C48_3 Comp 48
C60_1 Comp 60
C60_2 Comp 60
C60_3 Comp 60
C72_1 Comp 72
C72_2 Comp 72
C72_3 Comp 72
C96_1 Comp 96
C96_2 Comp 96
C96_3 Comp 96
I0_1 Incomp 0
I0_2 Incomp 0
I0_3 Incomp 0
I6_1 Incomp 6
I6_2 Incomp 6
I6_3 Incomp 6
I12_1 Incomp 12
I12_2 Incomp 12
I12_3 Incomp 12
I18_1 Incomp 18
I18_2 Incomp 18
I18_3 Incomp 18
I24_1 Incomp 24
I24_2 Incomp 24
I24_3 Incomp 24
I30_2 Incomp 30
I30_3 Incomp 30
I36_1 Incomp 36
I36_2 Incomp 36
I36_3 Incomp 36
I42_1 Incomp 42
I42_2 Incomp 42
I42_3 Incomp 42
I48_2 Incomp 48
I48_3 Incomp 48
I60_1 Incomp 60
I60_2 Incomp 60
I60_3 Incomp 60
I72_1 Incomp 72
I72_2 Incomp 72
I72_3 Incomp 72
I96_2 Incomp 96
I96_3 Incomp 96
Here, to "control" are actually the 0 time points from both "compatible" and "incompatible". And I would like to compare:
- the differentially expressed genes between 'compatible' and 'incompatible' at each time point
AND
- the differentially expressed genes within the time points (e.g. Comp_6_vs_Comp_0)
I hope i am clear enough,
Thanks in advance
Cecile
