DESeq2 One-way ANOVA with 3 sample groups?
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@alexpelletier-6758
Last seen 6.0 years ago
United States


I'm trying to use DESeq2 to perform something like a one-way ANOVA on 3
groups of samples. I've seen references to DESeq2's capability of
performing similar ANOVAs such as this forum thread:
http://seqanswers.com/forums/showthread.php?t=16539

However, I can't seem to find anything in DESeq2's manual about how to
do this. I have my data inputted successfully, and I've been able to
perform pairwise comparisons using DESeq2 but I haven't been able to
extract one p-value across 3 different groups. Is there somewhere that
explains this functionality? Or some sort of example code run through?
Thanks for your help.

deseq2 Anova • 7.1k views
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@mikelove
Last seen 3 days ago
United States

The likelihood ratio test will give you a single p-value for the removal of a variable from the design. 

For example, if 'group' is a factor in colData(dds) with three levels:

design(dds) = ~ group
dds = DESeq(dds, test = "LRT", reduced = ~ 1)
results(dds)

See the likelihood ratio section of ?DESeq and ?nbinomLRT for more information.

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@Michael Love,

I have a follow-up question here on DESeq2 One-way ANOVA with 3 sample groups. I honestly speaking did not understand well how this One-way ANOVA works here. Basically, my question is I would like to do get differentially expressed genes in one condition compared to the other two conditions. This means I have three groups(Cancer_Staging_1, Cancer_Staging_2, and Cancer_Staging_3). I want to see genes specifically expressed in Cancer_Staging_1 considering Cancer_Staging_2 and Cancer_Staging_3as a comparison group at a time.

Best, AD

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You can do two pairwise comparisons and take the intersection.
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