I am trying to follow the data cleaning workflow published in "A cross-package Bioconductor workflow for analyzing methylation array data", however some of the analyses require a sample sheet containing the sample source and sample group for each sample. I downloaded my methylation data from the GDC legacy archive, which does not allow you to download a sample sheet. Any way I can work around this and obtain the sample source and sample group data that I need?
You mean this tutorial: A cross-package Bioconductor workflow for analysing methylation array data
I would just create a custom sample sheet with minimal information. In it, you can also encode certain groups in relation to your samples. I believe it likely that much of the information, like
Slide, et cetera, will never be used.