Manual Clustering 2

Manual Clustering, Continued Alright, some updates from last time: Rather than setting the number of modules independently for each individual crab/transcriptome, I specified a single cut height, which was used on the dendrogram for each crab to separate into modules. For crabs A-F (where three time points are present), this cut height was 1.8, and was chosen because it generally separated crabs into 5-8 modules, all of which appeared to contain single expression patterns. Crabs G, H, and I were part of the elevated-temperature treatment group, which only had 2 time points, and so that cut height just wasn’t adequate. As a result, for these crabs, I bumped up the cut height to 10. These changes can be seen in scripts 71-73. All are the same except for initial inputs and module naming but here’s one as an example I changed my name scheme for the manual clustering method. Previously,…

from Aidan F. Coyle