Question: DESeq2 result contrast
0
gravatar for hamsasekar02
4 weeks ago by
hamsasekar020 wrote:

I have three genotypes (I,II,III) and conditions (infected,mock)

When i do the DESeq2 analysis with model Genotype+condition+Genotype:condition I get the following result

[1] "Intercept"                        "Genotype_II_vs_I"          
[3] "Genotype_III_vs_I"             "condition_infected_vs_mock"      
[5] "GenotypeII.conditioninfected" "GenotypeIII.conditioninfected"  

results(dds, contrast=list( c("condition_infected_vs_mock","GenotypeII.conditioninfected")))

Does this me the result in GenotypeII after comparing with GenotypeI in infected vs mock condition I want to compare Genotype II with GenotypeI in infected vs mock condition

R • 151 views
ADD COMMENTlink modified 4 weeks ago by ATpoint15k • written 4 weeks ago by hamsasekar020

It's a bit unclear exactly what you want to compare. Is it GenotypeII vs. GenotypeI while controlling for condition? If so you don't need a contrast, it's the Genotype_II_vs_I coefficient.

ADD REPLYlink written 4 weeks ago by Devon Ryan89k

Thank you Sir for the reply To make it more clear, I want to compare Genotype II vs Genotype I in infected vs mock condition, and also seeing the condition effect of GenotypeII with respect to Genotype I

ADD REPLYlink written 4 weeks ago by hamsasekar020

I count more than one comparison in that sentence, rephrase it to include only one. You can control for various effects, but you can only extract one comparison at a time.

ADD REPLYlink written 4 weeks ago by Devon Ryan89k

Thank you Sir, I understood that ("GenotypeII.condition infetced") will give me difference in in mock vs infected samples of GenotypeII taking care of mock vs infected levels in the reference genotype (Genotype I) . Is my understanding correct ??

ADD REPLYlink written 4 weeks ago by hamsasekar020
1

Yes, stated differently that's the excess effect of having both GenotypeII and being infected at the same time compared to what you would expect if GenotypeII and "infected" didn't interact with each other at all.

ADD REPLYlink written 4 weeks ago by Devon Ryan89k
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