edgeR: is calcnormfactors necessary for complex GLM approach?

Question

[Biogeek]

Hi,

As the topic asks. Is calcnormfactors function necessary to run pre complex GLM in edgeR (referring to 3.2.3 of the vignette). I'm confused, does the GLM normalize the data itself?

Answer 1

[Devon Ryan]

Yes, you must compute normalization factors before doing a GLM analysis.

[Biogeek]

Thanks for confirming Devon.

I used: calcNormFactors(matrix, method=c("TMM")

Is this suffice?

Thanks.

[Devon Ryan]

Yup, that should do it.