Hello everyone!

I was working with TCGA/GDC methylation level 3 data (RangedSummarizedExperiment, downloaded with TCGAbiolinks). However, every time I ran the champ.filter() function, the detP parameter switched from TRUE to FALSE. This makes sense, considering that I don't have a basis for it. I've checked the number of probes in the methylation matrix, which is theoretically pre-processed, but noticed that the total number of probes doesn't undergo a pre-filtering step as this matrix has all 450k array probes. With that in mind, I am thinking of starting the analysis from scratch (i.e., using the .idat files). However, when we downloaded these files, I didn't have a pd file necessary as input for champ.load() function. Am I mistaken? Do you have any suggestions?

Many thanks!