Hey everyone,

I'm really new to R (first week!) and am trying to develop a script to analyse my DNA Methylation data.

I began with the minfi package initially and everything worked smoothly there, but I've been getting stuck with Champ. To start with, I've been having trouble loading in the data set.

Below, you can see the code I'm using ("filepath" meaning my file directory, which works fine), and the Error message it generates. I've already looked online and can't find any info on it. Can anyone make any recommendations?

Cheers!

# Code

testDir=file.path("filepath")
myLoad <- champ.load(testDir,arraytype="450k")

# Error Message

Error in if (any(numfail >= SampleCutoff)) { :
missing value where TRUE/FALSE needed

Hi,

Are you using EPIC or 450k array ? Because it seems this issue occurs when we set the wrong arratype.

Try

myLoad <- champ.load("raw/",arraytype="EPIC")