Hi,
I'm looking for some help on the analysis of a multi-factor design with DESeq2.
I have a 4-factor experiment:
Groups: A (8 Donors), B (4 Donors), C (4 Donors), D (4 Donors)
Treatment: Control vs Infection
Time: 8h, 16h, 24h
The approach I took was combining all 3 factors (Group, Treatment, Time) into a single factor and using design=~ Donor + Group_Treatment_Time.
Then I looped through time points and through treatments to get differential expressed genes between two groups for each treatment and time-point:
res <- results(dds, c("Group_Treatment_Time", paste("A", treatment, timepoint, sep="-"), paste("B", treatment, timepoint, sep="-")))
However, I want to take advantage of the time course. In particular, I'm interested in time-specific differences:
i) between control and infection for each group
ii) between groups for control (or infection)
and I'm interested in finding genes with a difference in baseline expression (a main effect), ie lines moving in parallel:
iii) between control and infection for each group
iv) between groups for control (or infection)
My questions are:
1) Should I use a different design and LRT to find all genes with time-specific differences? How should that design be with 4 different factors?
2) How should I set up the contrasts for the cases i) to iv)?
Thank you so much for your help! I've read the vignette, many threads on the web, and talked to a couple of colleagues but I am still confused about how to run this analysis.
Regards,
Ana
I'm looking for some help on the analysis of a multi-factor design with DESeq2.
I have a 4-factor experiment:
Groups: A (8 Donors), B (4 Donors), C (4 Donors), D (4 Donors)
Treatment: Control vs Infection
Time: 8h, 16h, 24h
The approach I took was combining all 3 factors (Group, Treatment, Time) into a single factor and using design=~ Donor + Group_Treatment_Time.
Then I looped through time points and through treatments to get differential expressed genes between two groups for each treatment and time-point:
res <- results(dds, c("Group_Treatment_Time", paste("A", treatment, timepoint, sep="-"), paste("B", treatment, timepoint, sep="-")))
However, I want to take advantage of the time course. In particular, I'm interested in time-specific differences:
i) between control and infection for each group
ii) between groups for control (or infection)
and I'm interested in finding genes with a difference in baseline expression (a main effect), ie lines moving in parallel:
iii) between control and infection for each group
iv) between groups for control (or infection)
My questions are:
1) Should I use a different design and LRT to find all genes with time-specific differences? How should that design be with 4 different factors?
2) How should I set up the contrasts for the cases i) to iv)?
Thank you so much for your help! I've read the vignette, many threads on the web, and talked to a couple of colleagues but I am still confused about how to run this analysis.
Regards,
Ana
