Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data [Methylomics]

We experimented how well various supervised machine learning methods such as decision tree, partial least squares discriminant analysis (PLSDA), support vector machine and random forest perform in classifying endometriosis from the control samples trained on both transcriptomics and methylomics data. The assessment was done from two different perspectives for improving classification performances: (a) implication of three different normalization techniques, and (b) implication of differential analysis using the generalized linear model (GLM). We concluded that an appropriate machine learning diagnostic pipeline for endometriosis should use TMM normalization for transcriptomics data, and quantile or voom normalization for methylomics data, GLM for feature space reduction and classification performance maximization. Total 77 MBD-seq samples were analyzed where 35 were control and 42 were disease samples Please note that GSE134056 records represent the transcriptomics data.