edgeR supports continuous covariates?
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Ivy • 0
@user-24077
Last seen 2.2 years ago

Thanks for preparing the guideline on edgeR. However, I did not see any information supporting continuous variables in edgeR. May I know does edgeR supporting below 2 situations:

(1) 2 group comparison with adjustment of1 or 2 continuous covariates? (2) Association analysis of gene with one continuous variable? Thanks!

edgeR • 1.2k views
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Yunshun Chen ▴ 780
@yunshun-chen-5451
Last seen 3 months ago
Australia

edgeR can handle time-course experiments where time is considered as a continuous variable. Please refer to the time course case study in the user's guide. The cubic spline approach can be applied to continuous variables other than time.

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Hi Yunshun Chen and Gordon Smyth,

Thanks for the quick response. It would be highly appreciated if you can explain a little bit further.

I see poly(Hours, degree = 3) and ns(Hours, df =3) before constructing the design matrix in the user's guide. Are there any reason in using this transformation of continuous covariate? Why cubic spline is suggested to continuous variable? I am confused in which df can be used in ns().

Furthermore, as Gordon Smyth suggested here "edgeR can handle any linear model with any combination of continuous covariates or factors. Any model that can be created by model.matrix can be fitted by edgeR."

Is that ok to use the following code directly to both factor covariate and the continuous covariate analysis? Much appreciated!

d <- edgeR::calcNormFactors(d)
design <- model.matrix(~covariate)
rownames(design) <- colnames(d)
d <- estimateDisp(d, design, robust=TRUE)
fit <- glmFit(d,design)
res <- glmLRT(fit)

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@gordon-smyth
Last seen 4 minutes ago
WEHI, Melbourne, Australia

edgeR can handle any linear model with any combination of continuous covariates or factors. Any model that can be created by model.matrix can be fitted by edgeR.

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Hi Yunshun Chen and Gordon Smyth, does edgeR support mixed model? (https://en.wikipedia.org/wiki/Mixed_model)