How to dissect the tumors

1. check batch effect in SGIIA
(1) Heatmap, PCA on control genes
(2) Define the batches by global PCA
2. ComBat
3. CC_IFS on SGIIA
4. Select samples with avg_consensus_idx > 0.9
5. Use samples from step 4, and combine with SGIIB samples, repeat step 2-4
6. For new cohorts, repeat step 5.

limma to derive pairwise siganture, use NTP or SVM to predict.