DESeq2: Getting results from multiple comparisons

Question

[rus2dil]

Hello, I have following as my experimental design in DESeq2 and I am wondering how to retrieve results for all the pairwise comparisons.

Design

Genotype | Days
WT 50
WT 100
WT 200
A 50
A 100
A 200
B 50
B 100
B 200

Default resultsnames are

Intercept
Genotype_A_vs_WT
Genotype_B_vs_WT
Days_100_vs_50
Days_200_vs_50
GenotypeA.Days100
GenotypeB.Days100
GenotypeA.Days200
GenotypeB.Days200

How do I retrieve results for
1. WT.50 vs A.50, WT.50 vs B.50, A.50 vs B.50 and similar comparisons for 100 and 200 days?
2. WT.50 vs WT.100, WT.56 vs WT.100, WT.100 vs WT.200 and similar results for Genotypes A and B?

Answer 1

[swbarnes2]

I hope you have a few replicates for each genotype and day combination. If you really only have 9 samples you can't do those comparisons. But if have replicates, make a new column that has genotype and days stuck together. Make that column name your design. You can specify whatever contrast you want when calling for the results, even if it's not in resultsNames.