Table 3.
Key parameters utilized in four independent analyses.
| 1.0 threshold to raw signals, 90 percentile shift normalization to all samples, 31181_v18_0 technology | |||||||
|---|---|---|---|---|---|---|---|
| Analysis 1 | Analysis 2 | Analysis 3 | Analysis 4 | ||||
| N-NT vs. CTT vs. D-NT vs. necrosis | CTT vs. D-NT | ICC (CTT + D-NT) vs. N-NT | Well differentiated vs. papillary vs. moderately differentiated | ||||
| Well differentiated CTT vs. D-NT | Papillary CTT vs. D-NT | Moderately CTT vs. Nec vs. D-NT | Well differentiated (CTT + D-NT) vs. N-NT | Papillary (CTT + D-NT + Nec) vs. N-NT | Moderately differentiated (CTT + D-NT + Nec) vs. N-NT | Well differentiated (CTT + D-NT) vs. Papillary (CTT + D-NT + Nec) vs. Moderately differentiated (CTT + D-NT + Nec) | |
| 3D PDA | Raw value > 30 | Raw value > 20 | Raw value > 30 | Raw value > 30 | |||
| Raw > 30 | Paired t-test, p < 0.05 | Paired t-test, p < 0.05 | N/A | unpaired t-test, Benjamini Hochberg FDR correction, p < 0.01 | unpaired t-test, Benjamini Hochberg FDR correction, p < 0.005 | unpaired t-test, Benjamini Hochberg FDR correction, p < 0.005 | Fold change (FC) > 2 in 2 pairs |
| Hierarchical clustering, | FC > 2 | FC > 4 in 2 pairs | FC > 2 | One-way ANOVA, Benjamini Hochberg FDR correction, p(corr) < 0.05 | |||
| Euclidean distance metric, Median linkage rule | |||||||
| One-way ANOVA, p < 0.05 | |||||||
Abbreviations are as follows: Intrahepatic cholangiocarcinoma tumor tissue (CTT); distal non-tumor tissue (D-NT); and normal non-tumor tissue (N-NT).