Multifactor design result extraction in voom limma
I have successfully carried out all the steps of differential expression analysis using voom-limma with the following design:
~Genotype + Treatment + Genotype:Treatment
where, Levels of Genotype: WT, KO; Levels of Treatment: Naive, Morphine
I am familiar with extracting a result (Effect of knock out under Morphine treatment) in DESEq2 Multifactor design, which is as follows:
KO_vs_WT_in_Morphine <- results(dds, contrast = list(c('Genotype_KO_vs_WT', 'GenotypeKO.TreatmentMorphine')))
Could someone please help me out with doing the same in voom limma? I tried the following, but am not sure whether I'm doing it correctly:
KO_vs_WT_in_Morphine <- topTable(fit, coef=c("GenotypeKO" , "GenotypeKO:TreatmentMorphine"))
Is specifying a vector for coef parameter okay? Or is there a better way to go about it?
Thank you!
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aarthir239 •
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Wouldn't it be clearer to not use an intercept and then directly contrast the groups rather than coefficients?