Hi list, I used methylumi to analysis my Illumina GoldenGate methylation data. The data are for two disease status, I want to find the different methylation genes in the two disease status. All sample are done in two array. I used qcplot find that hybridization controls failed for lots of samples. signi cantly poorer quality are removed. When I set toKeep <- (avgPval < 0.05), there are 133 samples remained. If I set toKeep <- (avgPval < 0.005), there are 69 samples remained. After I used limma to find the different methylated genes. But for different avgPval cutoff value, the genes I found is very different. So which one should I trust? Any comments? Thanks.