ahg12441-sup-0001-FigureS1.pdf249.6 KB Supplementary Figure S1. Effect of different fold change thresholds on DEG identification for the three cancer types. ahg12441-sup-0002-FigureS2.pdf115.3 KB Supplementary Figure S2. Effect of different FDR thresholds on DEG identification for the three cancer types. ahg12441-sup-0003-FigureS3.pdf155.8 KB Supplementary Figure S3. Evaluation of overlap rates depending on biological replicate numbers for different fold change thresholds. ahg12441-sup-0004-FigureS4.pdf155.9 KB Supplementary Figure S4. Evaluation of overlap rates depending on biological replicate numbers for different FDR thresholds. ahg12441-sup-0005-FigureS5.pdf514.8 KB Supplementary Figure S5. FPKM values of the top 10 up- and down-regulated DEGs of repeat I for n = 20 in BRCA. ahg12441-sup-0006-FigureS6.pdf545.5 KB Supplementary Figure S6. PCA plots for each cancer type comprising all samples used in the study. ahg12441-sup-0007-FigureS7.pdf76.8 KB Supplementary Figure S7. Mean number of DEGs detected using different threshold levels for the Hela cell line. ahg12441-sup-0008-FigureS8.pdf98 KB Supplementary Figure S8. Evaluation of overlap rates depending on biological replicate numbers for different threshold levels. ahg12441-sup-0009-FigureS9.pdf611.4 KB Supplementary Figure S9. TMM-normalized read count values of the top 10 up- and down-regulated DEGs of repeat I for n = 20. The raw read counts of the five genes (IDO1, LGALS17A, PLAAT4, GBP4, and IFI44L) are 0 for all the 20 samples of the naïve cell group studied. ahg12441-sup-0010-FigureS10.pdf142.5 KB Supplementary Figure S10. Sensitivity and specificity of DE results for FDR (0.05) and FDR (2–n). ahg12441-sup-0011-FigureS11.pdf2.5 MB Supplementary Figure S11. ROC curves for different numbers of biological replicates for the three cancer types studied. Each curve is calculated by varying the FDR parameter between 0 and 1 using the plotROC package in R. To clearly distinguish one curve from another, the curves for the four repeats of each n are presented separately for each cancer type, i.e., (a, e, i) show the curves for repeat 1 of each n, (b, f, j) show the curves for repeat 2 of each n, (c, g, k) show the curves for repeat 3 of each n, and (d, h, l) show the curves for repeat 4 of each n. ahg12441-sup-0012-FigureS12.pdf3.6 MB Supplementary Figure S12. ROC curves for the four repeats of each n for BRCA. The black dot on each curve represents the optimal cutpoint of FDR threshold which is calculated using the coords function of pROC package in R. The optimal cutpoint value of FDR threshold for each curve is provided and the corresponding values of sensitivity and specificity of the optimal cutpoint are given in parentheses. ahg12441-sup-0013-FigureS13.pdf2.6 MB Supplementary Figure S13. ROC curves for the four repeats of each n for KIRC. The black dot on each curve represents the optimal cutpoint of FDR threshold which is calculated using the coords function of pROC package in R. The optimal cutpoint value of FDR threshold for each curve is provided and the corresponding values of sensitivity and specificity of the optimal cutpoint are given in parentheses. ahg12441-sup-0014-FigureS14.pdf1.5 MB Supplementary Figure S14. ROC curves for the four repeats of each n for LUAD. The black dot on each curve represents the optimal cutpoint of FDR threshold which is calculated using the coords function of pROC package in R. The optimal cutpoint value of FDR threshold for each curve is provided and the corresponding values of sensitivity and specificity of the optimal cutpoint are given in parentheses. ahg12441-sup-0015-FigureS15.pdf442.4 KB Supplementary Figure S15. The optimal cutpoint values of FDR threshold for the four curves of each n for BRCA (a), KIRC (b), and LUAD (c). The red diamond denotes the mean of the four optimal cutpoint values of FDR threshold for each n. ahg12441-sup-0016-TableS1.rds1.7 MB Supplementary Table S1. VennCount table of DEG lists obtained by (FDR (0.001), LFC (4)) for n from 3 to 24 for BRCA. ahg12441-sup-0017-TableS2.txt2.7 MB Supplementary Table S2. VennCount table of DEG lists obtained by (FDR (0.001), LFC (4)) for n from 3 to 18 for KIRC. ahg12441-sup-0018-TableS3.txt135 KB Supplementary Table S3. VennCount table of DEG lists obtained by (FDR (0.001), LFC (4)) for n from 3 to 14 for LUAD. ahg12441-sup-0019-TableS4.docx23.7 KB Supplementary Table S4. The ranks of the 10 top DEGs for each repeat in the three other repeats for n = 20 in BRCA. ahg12441-sup-0020-SuppMat.txt43.1 KB Supplementary information