Kaitlyn’s notebook: clustering without day 0

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.

 

Scree plot

Dendrogram

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