Entering edit mode
4 months ago
Hello everyone, Currently I'm a beginner in the world of methylation analysis. I am pre-processing the raw data sets and extracting methylation data via bismark. In downstream, I use several R/Bioconductor packages to analyse the data. But almost every package page starts with the sentence "A tool to analyse WGBS" or "A tool to analyse xxx array data". Is there such a difference? Can't I use a package designed for array data for WGBS or any other data? I know the final bismark file is universal but these statements are so confusing. Thanks in advance.
Most statistical approach to detect differentially methylated positions/regions would be the same indeed. However, arrays should follow specific normalization steps due to their particular construction (dye bias, type I/II bias, etc...). So it will depend on what steps you want to apply to your dataset.