Fig. 1
Relationship between the shape of HSC and DE results. a HSC dendrogram for Blekhman data consisting of 16,560 genes × 18 samples. The clustering was performed using the “clusterSample” function with default options in TCC. The unique filtering (from 17,886 genes to 16,560 genes with unique expression patterns across 18 samples) was internally performed in the function to reduce the negative effect on associations in low count regions when calculating Spearman’s r as a distance measure. b DE results from a total of 15 two-group comparisons with three replicates. The DE pipeline provided in TCC was applied to the Blekhman’s count matrix consisting of 17,886 genes after zero-count filtering. The PDEG values and AS values for individual comparisons are provided on the right