Fig. 2

Benchmark dataset construction: a 5 different cell populations present in pancreatic tumors were considered. b Raw transcriptome and methylome profiles of these different cell populations were extracted from various sources (PDX model, tissues or isolated cells). c Raw cell type profile matrices were preprocessed together (Feature filtering, normalization, signal transformation, sample aggregation) to avoid any batch effect. After pre-processing, transcriptomic data are constituted of log2-transformed expression counts on 21,566 genes and methylome data of beta-values on 772,316 EPIC array CpG sites. d In silico Dirichlet distributions have been used based on realistic proportions defined by the anatomopathologist expertise (J. Cros). e Paired methylome and transcriptome of in silico mixtures from pancreatic tumors were obtained by considering D = T × A, with T the cell-type profiles (matrix of size M × K, with M the number of features and K = 5 the number of cell types) and A the cell-type proportion per patient (matrix of size K × N, with N = 30 the number of samples) common between both omics. One training set (D_MET and D_RNA) is accessible to the users (obtained by one realization of A). The algorithms are compared on 10 test sets (obtained from 10 other realizations of A) that are hidden on the platform