I'm using the champ.load to read and filter my data and it works well. However when I want to proceed with the champ.QC I receive an error because the column "Sample_Group" in the csv file provided is empty.
So I tried to add the information of that column ("first" or "second") and use the modified csv file to load the idat files. However at that point I'm getting the following error:
"Error in champ.import(directory, arraytype = arraytype) : Error Match between pd file and Green Channel IDAT file."
I went through the pipeline to check how ChAMP imports the data but I did not manage to pick which is the mistake. I know It would be great if you could help so that I can include this information and proceed with champ.QC.