Hi,
I am running DESeq2 to get DEGs from experiment below. The experimental design I am working on has three factors with respective levels:
- Time (1dpi, 4dpi)
- Cultivar (J, Q, R)
- Treatment (infected, control)
time cultivar treatment
1dpi J control
1dpi J control
1dpi J control
4dpi J control
4dpi J control
4dpi J control
1dpi J infected
1dpi J infected
1dpi J infected
4dpi J infected
4dpi J infected
4dpi J infected
1dpi Q control
1dpi Q control
1dpi Q control
4dpi Q control
4dpi Q control
4dpi Q control
1dpi Q infected
1dpi Q infected
1dpi Q infected
4dpi Q infected
4dpi Q infected
4dpi Q infected
1dpi R control
1dpi R control
1dpi R control
4dpi R control
4dpi R control
4dpi R control
1dpi R infected
1dpi R infected
1dpi R infected
4dpi R infected
4dpi R infected
4dpi R infected
Actually, I am interested in DEGs responding to infection over time in cultivars. So, first I used a design of ~ Treatment + Cultivar + Time + Time:Treatment + Cultivar:Treatment
, but one of my colleague suggested me to include the three way interaction (Treatment:Cultivar:Treatment) to this design to include all the interaction of the factors.
Now, I am struggling with these issues:
Which of the design formula answer the question (DEGs responding to infection over time in cultivars) I am looking for? design formula above or inclusion of three-way interaction to the formula?
Does factor grouping (considering cultivar and time as one factor called
group
) work to answer the question? for example,~ group + treatment + group:treatment
If none of above possibilities work, is there any way to get DEGs responding to infection over time in cultivars.
Any help is greatly appreciated.
Best, Nourolah
Thanks Michael for your response.
Is there anyway in DESeq2 to determine the statistical significance of individual factors or their interaction in these type of multifactor design?
Thanks.
Yes, take a look at ?results
My appology for asking another question!
Baesd on above biological question and when I used the code below:
the output of
resultsNames(dds)
is:1) Why in coefficients [9] and [10] is there
control
, because I have defined it beforehand as the reference level?2) And, by looking at the DEGs (below) of for example [12] and [10] it seems the reference level have not been considered in the three-way interaction (please correct me if I am wrong). So, how should these [11] versus [9], and [12] versus [10] be treated if I am going to see the effect of infected versus control?
In advance I appreciate your helps!
This is beyond the scope of the support I can provide here, that is, interpretation of individual terms in a complex design, and how choice of design influence the meaning of these terms.
I'd recommend to meet with a statistician and you can discuss what these terms represent.