Additional file 13 of Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets

Additional file 13: Table S12. Relevance of pathways enrichment after quality imbalance mitigation. Mitigation of quality imbalance was performed either within the differential analysis (using low-quality probabilities of the samples, Plow values, as covariates in DESeq2) or by removing quality outlier samples (based on Plow values). First, pathways associated with low-quality markers (low-quality pathways) were derived for various reference gene lists of the MSigDB database (column gene_sets). For each dataset, a gene set enrichment analysis was performed on differential genes (differential pathways) with a positive or negative log-fold change (pos and neg values in column deg_sign, respectively). We summarized results only for datasets for which at least 1 low-quality pathway overlaps with differential pathways (n_datasets) and counted the number of datasets where the mitigation method had positive (column better), negative (column worse), or no substantial impact (column no_change).