champ.norm error

I am running a methylation data analysis using ChAMP package. I did champ.load from .idat files and now am trying to do champ.norm with BMIQ method and get the following error:

Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x],  : 
  task 165 failed - "need at least 2 points to select a bandwidth automatically"

How do I fix it?

methylation normalization bmiq champ champ.norm

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updated 3.7 years ago by Ram

• written 3.7 years ago by bioLearner •

Could you check colSums(is.na(beta)) ?

• 0 views • link

written 3.7 years ago by Basti •

Yes! I checked

sum(is.na(myLoad$beta)) 
any(myLoad$beta == 0)

and there were none

• 0 views • link

updated 3.7 years ago by Ram

• written 3.7 years ago by bioLearner •

0 answers

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