Question: DESeq2: Getting results from multiple comparisons
0
gravatar for rus2dil
29 days ago by
rus2dil20
Sri Lanka
rus2dil20 wrote:

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?

rna-seq contrasts deseq2 • 78 views
ADD COMMENTlink modified 29 days ago by swbarnes28.1k • written 29 days ago by rus2dil20
0
gravatar for swbarnes2
29 days ago by
swbarnes28.1k
United States
swbarnes28.1k wrote:

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.

ADD COMMENTlink written 29 days ago by swbarnes28.1k
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