R Methy II: Packages

For this exercise, install the packages minfi and ChAMP. You find them on Bioconductor.

Install them using biocLite().

The Minfi-package has a not so complete Vignette, but this course material fills those gaps: https://www.bioconductor.org/help/course-materials/2015/BioC2015/methylation450k.html

Scripts

Since we will analyse the data using two different packages/pipelines, minfi and ChAMP, create two R scripts and call them e.g. minfi.R and champ.R. Use these scripts to write down all the analysis that you do in this exercise, then you can rerun your analysis if you have any problems on the way.

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