The results of the MeDIP-on-chip datasets support the conclusions reached for the ChIP-on-chip datasets: separation of the components present before normalization are preserved best with T-quantile and Tukey's biweight scaling approaches.
Another advantage of simulations is the controlled environment: one can select either the true, scattered, and random coincidences from the dataset, which allows separation of the different effects.
Pre-sorting of samples groups them by similar overall expression levels, reduces the complexity of the dataset and mimics separation of samples by condition.
Principal component analysis and Fisher linear discriminant analysis were then used to reduce the dimensions of the acquired dataset and quantify the separation of the protein classes, respectively.
Nevertheless, with a larger number of death events (419 versus 300) in this more mature dataset, a more evident separation of the survival curves is shown, the 95% CI around the HR is narrower, and the P value is now 0.092 (versus 0.151 previously; Figure 2A).
(C) Loadings of features in PCA of publicly available samples from four studies and the reported Indian cohort showing broad separation of one Chinese dataset comprising samples from patients with advanced gastric cancer.
(A) PCA of publicly available samples from four studies and the reported Indian cohort showing broad separation of a Chinese dataset comprising samples from patients with advanced gastric cancer.
Hence, one could still hope for a complete separation of the three classes when solving the LP for the entire dataset.
Considering the excitation spectra dataset alone, the HCA method revealed a successful separation of the four dyes, Fig. 5.
Different p-value transformations have been used to test the dendrogram robustness: dendrograms on datasets (columns) did not show changes in the whole structure but only on the bootstrap support (however, the first separation of datasets in two broad classes was always characterised by 100% bootstrap support).
