Table 1 An overview of the proposed data analysis workflow.
Steps | Detailed tasks | Comments |
|---|---|---|
Statement of the problem | • Specify comparisons of interest | • Express comparisons as statistical hypotheses |
|  | • Define scope of biological replication | • Restricted scope suitable for screening; expanded scope required for validation |
Exploratory data analysis | • Detect mis-identified features | • Remove obvious outliers |
|  | • Detect features with missing values | • Choose imputation strategy |
Model-based analysis | • Fit linear mixed model per protein | • Reduced scope of biological replication = fixed subjects; expanded scope = random subjects |
|  | • Check qq-plots plots for Normality | • If deviations, conclusions are approximate only |
|  | • Check residual plots for equal variance | • If deviations, use iterative least squares |
|  | • Test comparisons of interest | • Adjust p-values per comparison to control FDR |
|  | • Quantify protein abundance in conditions or samples of interest | • Use as input with downstream clustering or classification |
Design follow-up experiments | • Evaluate power and sample size | • Find minimal sample size for a fold change |
|  |  | • Find minimal fold change for a sample size |