Table 1. Main analysis customization input parameters and their default values (Full table of input options is presented in Supplementary Table S1).
Parameter | Default | Description |
---|---|---|
Clustering method | NONE | Cluster phospho-peptides using either PCA & k-means (19) or mclust (20) |
Ratio Cutoff | 3 | Threshold for phospho-peptide intensity ratio |
Correlation Method | Spearman | Choose correlation index among Spearman, Pearson and Kendall tau. |
Correlation Cutoff | 0.8–0.9 | Correlation coefficient threshold. Default 0.9 for Pearson, 0.8 for Spearman or Kendall tau |
Correlation P-value Cutoff | 0.05 | Threshold for significance of correlation of phospho-peptide profiles |