Table 2. The Effect of Normalization on the Prognostic Power of Expression Levels.

Normalization effect on significance of survival difference	CVRlow			CVRhigh			CVRrandom
	immune	non immune	total	immune	non immune	total	immune	non immune	total
Improved (LOD ≤ −2)	31	13	44	0	0	0	1	2	3
Degraded (LOD ≥ 2)	2	10	12	5	27	32	5	73	78

The counts represent the number of genes from each CVR group that had markedly different prognostic power in the raw and normalized datasets. For (p-normalized/p-raw), a LOD ≤ −2 represents a >7-fold decrease in p-value due to immFocus normalization, and a LOD ≥ 2 represents >7-fold increase in p-value (7-fold less significant) for gene expression predicting survival after immFocus normalization. The prognostic power was taken to correspond to the significance of the difference in survival between the upper and lower tertiles (in terms of expression level) of each gene. The log-rank test was used to determine the significance, applying the Bonferroni adjustment for multiple testing. Note that to consider only prognostic genes in this analysis, only genes that showed significant prognostic power in the raw and/or the normalized expression datasets, after Bonferroni adjustment, were considered.