Error when running ChAMP package

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hazel.rogers • 0

@hazelrogers-16030

Last seen 6.8 years ago

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 • 1.5k views

ADD COMMENT • link 6.8 years ago hazel.rogers • 0

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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 REPLY • link 6.8 years ago Yuan Tian ▴ 290

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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 REPLY • link 6.8 years ago hazel.rogers • 0

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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 REPLY • link 6.8 years ago Yuan Tian ▴ 290

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