Hi, I am working in champ Pipeline for processing methylation data. here is my code: library("ChAMP") myLoad <- champ.load('ADNI_iDAT_files',arraytype="EPIC") champ.QC(beta = myLoad$beta,pheno=myLoad$pd$Sample_Group) myNorm <- champ.norm(beta=myLoad$beta,arraytype="EPIC",cores=5)

but i get the error: [===========================]

[>>>>> ChAMP.NORM START <<<<<<]

champ.norm Results will be saved in ./CHAMP_Normalization/ [ SWAN method call for BOTH rgSet and mset input, FunctionalNormalization call for rgset only , while PBC and BMIQ only needs beta value. Please set parameter correctly. ]

<< Normalizing data with BMIQ Method >> Note that,BMIQ function may fail for bad quality samples (Samples did not even show beta distribution). Error in if (cores > detectCores()) cores <- detectCores() : missing value where TRUE/FALSE needed

i run the example file, using cores=5, it's ok . and library("doParallel") detectCores() , it's 40 . i try use 2 cores or 10 cores to run champ.norm in my own data, but got the same error. i'm confused. can any one help me to rectify this?

sincerely, mqyang