Question

Multiple comparisons in DESeq2

0

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thkapell ▴ 10

@tkapell-14647

Last seen 24 months ago

Helmholtz Center Munich, Germany

Hi,

I have a design like the one shown below and I want to test whether there are DE genes in condition 1 between Factor A, B and C (multiple comparisons). Is there a way to do this, other than performing all pairwise comparisons, e.g. B.1-A.1, C.1-A.1 and C.1-B.1?

Factor Condition

A 1

A 2

A 3

B 1

B 2

B 3

C 1

C 2

C 3

deseq2 • 684 views

ADD COMMENT • link updated 7.1 years ago by Michael Love 43k • written 7.1 years ago by thkapell ▴ 10

score 0 · Answer 1 · 2017-12-18

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Michael Love 43k

@mikelove

Last seen 13 hours ago

United States

Do you have replicates, or is the above table the colData of your experiment?

ADD COMMENT • link 7.1 years ago Michael Love 43k

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These are my different conditions. Yes, I have replicates on top of these (total number of replicates is 52).

ADD REPLY • link 6.9 years ago thkapell ▴ 10

1

Entering edit mode

You can do a likelihood ratio test. You can create a model matrix:

mm <- model.matrix(~condition + condition:factor)

Then you want to test the columns "condition1:factorB" and "condition1:factorC" at once. So you can use:

red <- mm[,-grep("condition1:", colnames(mm))]
dds <- DESeq(dds, test="LRT", full=mm, reduced=red)
res <- results(dds)

ADD REPLY • link 6.9 years ago Michael Love 43k