Question: cpg.annotate model requirements
gravatar for kadm
8 weeks ago by
kadm0 wrote:

I am using ChAMP to process EPIC methylation array data. While delving into the source code for champ.DMR for another reason, I noticed that it defined the linear model used in the DMRcate method as ~ pheno. Further delving revealed that champ.DMR calls DMRcate::cpg.annotate, which itself requires a model with an intercept (e.g. it is has this in the function stopifnot(colnames(design)[1] == "(Intercept)")).

Is there any way to circumvent this and input a model into DMRcate (and thus, into champ.DMR) that has no intercept, as in 0 + pheno? This is necessary as other methods (like champ.DMP) already use a no intercept model.

champ dmrcate • 92 views
ADD COMMENTlink modified 8 weeks ago by Yuan Tian110 • written 8 weeks ago by kadm0

You can specify contrasts=TRUE and pass a contrasts matrix (as you would in limma) to cpg.annotate; this will allow you to fit non-intercept models.


ADD REPLYlink written 7 weeks ago by Tim Peters80
Answer: cpg.annotate model requirements
gravatar for Yuan Tian
8 weeks ago by
Yuan Tian110
University College London
Yuan Tian110 wrote:

Hi, Kadm:

Sorry that ChAMP did not designed parameter to set intercept in DMRcate, thus I suggest you directly run DMRcate package with specific settings. The result should not be too hard to organize.

Best Yuan Tian

ADD COMMENTlink written 8 weeks ago by Yuan Tian110
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 310 users visited in the last hour