Hello Community, I am unable troubleshoot the following error shown below when trying to use champ.load() on IDAT files from Infinium MethylationEPIC Beadchip (v2).

Error in champ.import(directory, arraytype = arraytype) : Meth Matrix and UnMeth Matrix seems not paried correctly.

The console output shows that the data has 485512 Meth and UnMeth probes, so I do not understand how to troubleshoot this. I also keep getting this error below and am not sure whether it is related:

In readLines(csvfile) : incomplete final line found on '/PATH/data_test/EPICV2_208429680037.csv'

This is how my sample_sheet.csv is formatted (3 columns) and I made sure to have all corresponding .idat files for Green and Red

Sentrix_ID Sentrix_Position Sample_Group

123456789123 R01C01 Group1

123456789123 R02C01 Group2

...

I wasn't able to find a clear answer in other similar posts.

R script:

library(ChAMP) 
library(openxlsx) 

setwd("/PATH/data_test")

#load data 
myLoad_EPIC = champ.load(arraytype = "EPIC")  # arraytype = "EPICv2 was tried as well"

Error Output:

  Generating Meth and UnMeth Matrix
    Extracting Meth Matrix...
      Totally there are 485512 Meth probes in EPICv2 Annotation.
      Your data set contains 485512 Meth probes.
    Extracting UnMeth Matrix...
      Totally there are 485512 UnMeth probes in EPICv2 Annotation.
      Your data set contains 485512 UnMeth probes.

Error in champ.import(directory, arraytype = arraytype) : 
    Meth Matrix and UnMeth Matrix seems not paried correctly.
In addition: Warning message:
In readLines(csvfile) :
  incomplete final line found on '/PATH/data_test/EPICV2_208429680037.csv'