Thanks for reading, I would like to ask you for your opinion. I would like perform a methylation analysis comparing two groups of samples with a determined number of probes/genes, not using all the probes available in the array (this gene list comes from a literature search). My questions are:
- Should probe selection be done before the contrast? Reduce the number of probes to a few hundreds/thousands before any comparison.
- Should probe selection be done after the contrast? Use all the probes and do a heatmap, for example, only with selected probes.
- What statistical consequences any of this selections would have?
- Does anybody know how to perform the probe selection in a workflow using minfi/limma, for example? I am asking this because the annotation of the probes is done after performing the contrasts.
Any help will be much appreciated. Thanks