DESeq2 correct pairwise comparisions

Question

[hamsasekar02]

I have resultNames(dds) as -:

Model -

> dds <- DESeqDataSetFromMatrix(
+ countData = countTable,
+ colData = colTable,
design = ~ condition+time+condition:time)

> dds_lrt_time <- DESeq(dds, test="LRT", reduced = ~ condition + time)

> resultsNames(dds_lrt_time)
[1] "Intercept"                  "condition_infected_vs_mock"
[3] "time_4dpi_vs_2dpi"          "conditioninfected.time4dpi"

For a genotype I want to compare 4 dpi vs 2dpi in mock vs infected levels.

I have used condition_infected_vs_mock for DGEs for mock vs infected levels at 2dpi

condition_infected_vs_mock,conditioninfected.time4dpi for DGEs at mock vs infected levels at 4dpi

But now I want to compare infected vs mock levels at time 4dpi vs 2dpi

Can I use this interaction term conditioninfected.time4dpi for this comparison.

Answer 1

[Kevin Blighe]

Please take a look at my answer, here: A: DESeq2 compare all levels