Hello! I'm new to bioinformatics and I'm currently working on my first project using TCGA-UCEC DNA methylation data.

I'm downloading the data as a beta-value matrix, and I'm running into some confusion regarding preprocessing and analysis workflows. Most tutorials I find start from raw .idat files and use packages like minfi for preprocessing. However, since I only have beta-values, I believe I can't apply the standard minfi pipeline.

This leads to a couple of issues:

Many Bioconductor packages seem to expect minfi objects as input I'm unsure which preprocessing steps are still necessary (or appropriate) when starting from beta-values I’m also struggling with choosing reasonable cutoffs and parameter values without a clear reference workflow

I've tried exploring alternative approaches on my own, but I often feel lost without a standard pipeline to follow.

Is there a recommended workflow for analyzing TCGA methylation data starting from beta-values? Any guidance, references, or example pipelines would be greatly appreciated.