Question: order of covariates for GLM with edgeR
0
gravatar for aec
3.4 years ago by
aec40
aec40 wrote:

Hi,

I would like to know if the order of the covariates when constructing the design matrix for edgeR software matters.

For example:

design = model.matrix (~0+sex+batch+condition)

is the same as :

design = model.matrix (~0+condition+sex+batch)

thanks,

ADD COMMENTlink modified 3.4 years ago by Gordon Smyth37k • written 3.4 years ago by aec40
Answer: order of covariates for GLM with edgeR
2
gravatar for Aaron Lun
3.4 years ago by
Aaron Lun23k
Cambridge, United Kingdom
Aaron Lun23k wrote:

It won't affect dispersion estimation or fitting of the model, but it will affect how you parametrize your DE contrasts at the end. By default, glmLRT will drop the last coefficient; this will result in a different DE comparison between the two models, because the identity of the last term will be change when you mix up the order.

ADD COMMENTlink written 3.4 years ago by Aaron Lun23k

Ok, thanks for the clarification.

ADD REPLYlink written 3.4 years ago by aec40
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