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We downloaded the Infinium 450k beta value files for TCGA lung adenocarcinoma (LUAD) tumors using the ELMER packaged in Bioconductor . We removed any probe that did not have valid (non-NA) values for 2 or more of the LUAD samples and 2 or more of the healthy plasma samples. In order to make this analysis completely independent from the healthy lung epithelia deconvolution analysis, we excluded 488 CpGs that were included in the Megalodon "Two-component cell type methylation deconvolution using healthy lung epithelia" analysis above, and an additional 396 that were included in the DeepSignal analysis. We then performed a t-test to compare the methylation beta values of these LUAD-specific probes to the four plasma cfDNA samples from the MethAtlas paper , requiring a Benjamini-Hochberg corrected FDR of
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