I'm trying to replicate this paper (https://pathsocjournals.onlinelibrary.wiley.com/doi/10.1002/path.5845) and I don't understand this bit from the "Data Preprocessing" section on page 4:

Beta values whose corre-sponding intensities on probe-level failed a z-test with a P value threshold of 0.01 against background signal were masked.

Can someone please explain what this means? I'm using R, mainly minfi.

I'm trying to replicate this paper (https://pathsocjournals.onlinelibrary.wiley.com/doi/10.1002/path.5845) and I don't understand this bit from the "Data Preprocessing" section on page 4:

Beta values whose corre-sponding intensities on probe-level failed a z-test with a P value threshold of 0.01 against background signal were masked.

Can someone please explain what this means? I'm using R, mainly minfi.

Paper details:

Title: Machine learning models predict the primary sites of head and neck squamous cell carcinoma metastases based on DNA methylation

Details: It takes idat files from a few geo numbers for preprocessing and then models them. I have retrieved the idats from GEO used in the paper, fed them into minfi. My question is with the preprocessing while this data is in minfi.