I have several sets of Illumina data that assigning quality weights is appropriate for a limma analysis. While `arrayWeights` is very frequently used, I have noticed limma has the function `beadCountWeights` that appears to be performing quality weighting for BeadChips, but that function was never discussed here.
So, may I ask: For Illumina chips that have bead data (i.e. Avg_NBEADS and BEAD_STDEV) that can be extracted from GenomeStudio, which is the better way to calculate quality weights?