To evaluate the reproducibility, variability and signal-noise ratio between the five cell and RNA isolation methods, we examined variability between visits and probes. To explore visit variability (intra-individual), we calculated Spearman rank sum correlations between the two visits across all probes after applying two common probe filters (standard deviation (SD) and detection score). The correlations ranged between 0.86-0.92 for all probes, 0.83-0.90 for probes with SD > 0.5 and 0.90-1.00 for probes with detection score > 0.95 indicating a higher reproducibility between visits using the detection score as a probe filter (Table 1). These correlations (same individual) were higher than between random individuals. Although PAX showed a high reproducibility between visits, it provided significantly fewer detected probes (N = 8,783, 19%) than the other isolation methods (range = 10,672-12,122 probes, 23-26%; P < 1*10-16) (Table 1). The percentage of variable probes (SD > 0.5) in PAX, however, was significantly higher (73%) compared with the other methods (52%-65%; P < 1*10-16).
