Comparison Workflow Notebooks#
Inspect the notebooks associated with the imputation workflow.
Split creation and data handling
- Transfer data for NAGuideR format
- Experiment 03 - Data
- Arguments
- Raw data
- Machine metadata
- Select a subset of samples if specified (reduce the number of samples)
- First Step: Select features by prevalence
- Second step - Sample selection
- Sample Medians and percentiles
- Feature frequency in data
- Split: Train, validation and test data
- plot distribution of splits
- Save parameters
- Saved Figures
R models
Imputation model comparison
Differential Analysis Notebooks#
Inspect the notebooks associated with the differential analysis workflow.
Compare ANCOVAs
- PI vs Median
- Parameters
- Load scores
- Describe scores
- Load frequencies of observed features
- Compare shared features
- Plot qvalues of both models with annotated decisions
- Only features contained in model
- DISEASES DB lookup
- Shared features
- only by model
- Only by model which were significant
- Shared which are only significant for by model
- Only significant by RSN
- Write to excel
- Outputs
- PI vs VAE
- Parameters
- Load scores
- Describe scores
- Load frequencies of observed features
- Compare shared features
- Plot qvalues of both models with annotated decisions
- Only features contained in model
- DISEASES DB lookup
- Shared features
- only by model
- Only by model which were significant
- Shared which are only significant for by model
- Only significant by RSN
- Write to excel
- Outputs
- PI vs CF
- Parameters
- Load scores
- Describe scores
- Load frequencies of observed features
- Compare shared features
- Plot qvalues of both models with annotated decisions
- Only features contained in model
- DISEASES DB lookup
- Shared features
- only by model
- Only by model which were significant
- Shared which are only significant for by model
- Only significant by RSN
- Write to excel
- Outputs
- PI vs RF
- Parameters
- Load scores
- Describe scores
- Load frequencies of observed features
- Compare shared features
- Plot qvalues of both models with annotated decisions
- Only features contained in model
- DISEASES DB lookup
- Shared features
- only by model
- Only by model which were significant
- Shared which are only significant for by model
- Only significant by RSN
- Write to excel
- Outputs
- PI vs TRKNN
- Parameters
- Load scores
- Describe scores
- Load frequencies of observed features
- Compare shared features
- Plot qvalues of both models with annotated decisions
- Only features contained in model
- DISEASES DB lookup
- Shared features
- only by model
- Only by model which were significant
- Shared which are only significant for by model
- Only significant by RSN
- Write to excel
- Outputs
- PI vs DAE
- Parameters
- Load scores
- Describe scores
- Load frequencies of observed features
- Compare shared features
- Plot qvalues of both models with annotated decisions
- Only features contained in model
- DISEASES DB lookup
- Shared features
- only by model
- Only by model which were significant
- Shared which are only significant for by model
- Only significant by RSN
- Write to excel
- Outputs
- PI vs QRILC
- Parameters
- Load scores
- Describe scores
- Load frequencies of observed features
- Compare shared features
- Plot qvalues of both models with annotated decisions
- Only features contained in model
- DISEASES DB lookup
- Shared features
- only by model
- Only by model which were significant
- Shared which are only significant for by model
- Only significant by RSN
- Write to excel
- Outputs
Compare single differential analysis
Logistic regression models