Enter the body of text here

Code should be placed in three backticks as shown below

``Input- myNorm <- champ.norm(arraytype="EPIC") champ.SVD()

Corresponding output-

[>>>>> 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). 3 cores will be used to do parallel BMIQ computing. Warning message: In dir.create(resultsDir) : '.\CHAMP_Normalization' already exists

champ.SVD()

[<<<<< ChAMP.SVD START >>>>>]

champ.SVD Results will be saved in ./CHAMP_SVDimages/ .

Error in which(is.na(beta)) : object 'myNorm' not found In addition: Warning message: In dir.create(resultsDir) : '.\CHAMP_SVDimages' already exists ```

Query: We tried running this code and we got QC plots saved in a directory. But champ.SVD function fails to run, displaying the following error "Error in which(is.na(beta)) : object 'myNorm' not found". Kindly help me on the same.