User: Jeff Skinner

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Posts by Jeff Skinner

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Comment: C: Computing contrasts with a covariate using edgeR glmLRT()
... Thank you. This is what I was looking for. You are right that mean(X) isn't especially important, but it is a helpful way to code "compare the groups somewhere in the middle of the range of X" without specifying an exact X value. Usually the 3 places you would want to look are 1. Somewhere near min ...
written 2.2 years ago by Jeff Skinner0
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Comment: C: Computing contrasts with a covariate using edgeR glmLRT()
... Your advice to always use Age = 0 in my contrasts implies that I can only make contrasts at the Y-intercept. That's problematic if there is a significant Age*Class interaction, because the fold changes could change from minAge to meanAge to maxAge. Obviously, I should have specified the design as Y ...
written 2.2 years ago by Jeff Skinner0
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Answer: A: Computing contrasts with a covariate using edgeR glmLRT()
... Yeah, I noticed that after I posted it. Still, that would make the covariate coefficient of mean(Age) = 7.3 unnecessary, but it would not necessarily make the contrast itself nonsense. But suppose I had specified the interaction term here, would the contrast calculation represent an adjustment to ma ...
written 2.2 years ago by Jeff Skinner0
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Computing contrasts with a covariate using edgeR glmLRT()
... I'm using glmLRT() from edgeR to analyze some RNA-seq data. My experimental design has one Treatment factor with three classes (A, B and C), one continuous Age covariate and one Batch factor with 19 levels. > colnames(design) [1] "(Intercept)" "ClassB" "ClassC" "Age" ...
edger contrast covariate glmlrt() written 2.2 years ago by Jeff Skinner0

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