Gene expression differences between PAXgene and Tempus blood RNA tubes are highly reproducible between independent samples and biobanks

Table 2 Comparisons of results from statistical analyses (contrasts), “Focus of analysis” explains the focus of the comparison

Focus of analysis	Contrasts compared	Direction		Pearson	Spearman
Focus of analysis	Contrasts compared	Same	Opposite	Pearson	Spearman
Protocols used in exp. 1	c1 vs c2	1066	0	0.786	0.444
Protocols used in exp. 2	c3 vs c4	887	0	0.854	0.617
Reproducibility of the original protocol between exp. 1 and exp. 2	c1 vs c3	708	3	0.563	0.288
Reproducibility of the modified protocol between exp. 1 and exp. 2	c2 vs c4	417	0	0.604	0.222
Reproducibility of the modified protocol between exp. 1 and exp. 3	c2 vs c5	1199	8	0.681	0.313
Reproducibility of the modified protocol between exp. 2 and exp. 3	c4 vs c5	1330	0	0.857	0.487

“Comparison” specifies contrasts used in the comparison; see Table 1 and Fig. 1. “Direction” specifies if the significant probes (p < 0.05, Table 1) are expressed in the same or in the opposite direction between contrasts; hence, “Same” gives the number of probes where the logFC was positive or negative in both contrasts; “Opposite” gives the number of probes where the logFC was positive in one contrast and negative in the other. “Pearson” and “Spearman” give the Pearson and Spearman correlations, respectively, for the logFC values of all probes in the two contrasts used in the comparison

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