I have matrix of Beta values of methylation data using 450k array, I am using minfi to analyze the methylation data. I have the following questions:
1-How to normalize the data starting by Ratio Set. All normalization function use either RGChannelSet or MethylSet
2- I tried identification of DMR using bumphunter as follows:
designMatrix <- model.matrix(~ status)
#status is a factor with D and C levels for control and disease
dmrs <- bumphunter(GRset, design = designMatrix,cutoff = 0.2, B=0, type="Beta")
I got table with the following columns:
chr start end VALUE area cluster indexStart indexEnd L clusterL
What does the column VALUE means?
dmrs$pvaluesMarginal is empty with value NA
I do not know why dmrs$pvaluesMarginal is empty??
3-How to determine Hypo and hyper methylated genes?
Thank you very much in advance