Fig. 6
From: CoINcIDE: A framework for discovery of patient subtypes across multiple datasets
CoINcIDE versus concatenated results. Bar plots summarizing the counts for each PAM50 centroid subtype for each subtyping result from (a) PAM50 restricted 35-gene set CoINcIDE k-mean clustering, (b) concatenated matrix with no transformation, (c) concatenated matrix with gene-wise batch mean centering (BMC), and (d) concatenated matrix with ComBat. All analyses used k-means consensus clustering using the Proportion of Ambiguous Clusters (PAC) to select the number of clusters. These bar plots used only the 35-gene set to assign patients to PAM50 centroid subtypes (Additional file 1: Table S1). PAM50 centroid assignments were made on the pre-transformed concatenated datasets to allow for direct comparison between all four subtype discovery methods. See Additional file 3: Figure S9B for the corresponding CoINcIDE network figure for (a)