Question

DESeq2 Finding genotype effect to stimulation minus effect of not stimulating

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erin.gill81 ▴ 60

@eringill81-6831

Last seen 5.3 years ago

Canada

Hello,

I'm attempting to compare RNA-Seq datasets where I have two different genotypes (WT and mutant) and two conditions (stimulated and unstimulated). I would like to determine which genes are only differentially expressed between the two genotypes upon stimulation, but are NOT differentially expressed between the two genotypes when unstimulated. ie ((mutant.stimulated Vs WT.stimulated) Vs (mutant.unstimulated Vs WT.unstimulated)).

Is there a way to perform this comparison in DESeq2?

Thanks!

Erin

deseq2 rna-seq • 1.3k views

ADD COMMENT • link updated 8.9 years ago by Michael Love 43k • written 8.9 years ago by erin.gill81 ▴ 60

score 1 · Answer 1 · 2016-01-19

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Michael Love 43k

@mikelove

Last seen 15 hours ago

United States

hi Erin,

We don't have a way to compute a single contrast to build this set. You can however test for DE in stimulated, and then define an LFC threshold and test for log fold changes less than this in absolute value in unstimulated (see ?results arguments), and look at the overlap of the two sets of genes (defined by padj < FDR threshold in the two results tables).

ADD COMMENT • link 8.9 years ago Michael Love 43k

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And if you wanted to find genes which have a different fold change (mutant vs WT) in stimulated compared to unstimulated, you would simply add and test an interaction term between genotype and condition.