Question: DESeq2 design for time series data without "untreated"
0
gravatar for cecile.lorrain5
16 months ago by
cecile.lorrain50 wrote:

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

ADD COMMENTlink modified 16 months ago by Michael Love25k • written 16 months ago by cecile.lorrain50
Answer: DESeq2 design for time series data without "untreated"
0
gravatar for Michael Love
16 months ago by
Michael Love25k
United States
Michael Love25k wrote:

Hi Cecile,

Have you see the time series example in the workflow?

https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments

ADD COMMENTlink modified 16 months ago • written 16 months ago by Michael Love25k
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