Question: Error when running ChAMP package
0
gravatar for hazel.rogers
13 months ago by
hazel.rogers0 wrote:

I am trying to use ChAMP for analysis of my illumina 450K methylation data. I am a relatively inexperience R user. When I run the champ.QC() I get the following error.

Error in min(beta, na.rm = TRUE) : invalid 'type' (list) of argument

Could anyone tell me what this means and how I can correct it?

champ • 251 views
ADD COMMENTlink written 13 months ago by hazel.rogers0
Hello: This error indicates you have put wrong type of parameter into champ.QC(). I suspect the parameter is "beta" in your question. Could you tell me what is your beta matrix looks like and how did you generated it? Best Yuan Tian
ADD REPLYlink written 13 months ago by Yuan Tian110

Thank you for your reply. I'm not sure how to check what my beta matrix looks like. The code I have run to get to this point is

myLoad<-champ.load()

champ.QC(myLoad)

ADD REPLYlink written 13 months ago by hazel.rogers0

Hello:

Sorry that I was away to attend the examination in past 3 days.

I think you may try champ.QC() directly, instead of champ.QC(myLoad). Because champ.QC() take beta matrix in myLoad object to do analysis, instead of myLoad object itself. Thus I suggest you try it.

Or you may try:

champ.QC(myLoad$beta)

It should also work. Near all functions in ChAMP suppport solo beta matrix instead of over-complex objects.

Best

Yuan Tian

ADD REPLYlink written 13 months ago by Yuan Tian110
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