I redid the hierarchical clustering of the combined silo 3 and 9 datasheet without day 0.
Include Day 0 | Remove Day 0 | |
Agglomerate coefficient | 0.9964979 | 0.9976217 |
Cophenetic correlation | 0.9477519 | 0.9630485 |
Clusters | 41 | 84 |
Diferentially clustered proteins | 33 | 213 |
31 “diferentially clustered proteins” remained differentially clustered whether day 0 was included or excluded. So, removing day 0 causes more proteins to cluster separately (the agglomerate coefficient is slightly increased).
- i.e., removing day 0 causes more proteins to be identified as having different abundances.
- All abundances are the same for both silos on day 0 since no treatment had been administered yet.
- Removing day 0 means that only days following treatment are analyzed which makes more sense since we are attempting to identify proteins that have different abundances during treatment only.
- All abundances are the same for both silos on day 0 since no treatment had been administered yet.