DESeq2: experiment with two genotypes and three conditions
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efratk • 0
@efratk-22498
Last seen 4.3 years ago

Hi,

I have a question about an experiment with two genotypes: A, B and three conditions: C1, C2, C3. The design: ~ genotype + condition + genotype:condition

[1] "Intercept" "genotypeBvsA" "conditionC2vsC1" "conditionC3vs_C1"
[5] "genotypeB.conditionC2" "genotypeB.conditionC3"

How can be done the comparison between C3 to C2 in genotype B?

Thanks

deseq2 • 1.7k views
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@mikelove
Last seen 19 minutes ago
United States

Please see all of the examples that we have in the manual page for results().

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Hi,

I looked on the examples before and there is an example how to do the comparison of the interaction term for genotype effect in C3 vs C2: results(dds, contrast=list("genotypeB.conditionC3", "genotypeB.conditionC2")), but my question is how to do the comparison between C3 to C2 in genotype B and not the comparison of the interaction term. I did this comparison using grouping variable, but I would like to know how to do this comparison using interaction term in the design.

Thanks

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First take a look at the diagram in the vignette, which helps understand how interactions work.

If you have the C3 vs C2 difference between genotypes then you just add it to the main effect. You would add C3 vs C1 to the numerator and C2 vs C1 to the denominator.

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Thanks for the answer, I tried the comparison: contrast = list(c("conditionC3vs_C1","conditionC2vsC1")), but it didn't give me the right comparison, can you please tell me why is this

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That’s not it, I said you have to add that to what you had not replace with what you had.

Eg

list( c(“A”,”B”), c(“C”,”D”) )

This puts A and B in numerator and C and D in denominator. Take a look at the Examples section of

?results

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OK, thank you very much.

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Dear Michael

I have a similar problem as efratk. See:

https://www.biostars.org/p/426021/#426100

I tried to understand the example in ?results, but I cannot figure out how to apply it to my problem.

Any suggestions, would be really appreciated.

Thank you in advance.

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If the examples in ?results and the diagram in the vignette don't help, I recommend to consult with a statistician, or anyone familiar with linear models in R. There should be someone at your institute who can help walk you through it.

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