Table of contents:
- Overview
- Performance Plots
- Performance of PETfold_pre2.0(seed)
- scored higher in this pairwise comparison
- Performance of Alterna
- scored lower in this pairwise comparison
- Compile and download dataset for PETfold_pre2.0(seed) & Alterna [.zip] - may take several seconds...
Overview
| Metric |
PETfold_pre2.0(seed) |
|
Alterna |
|---|
| MCC |
0.736 |
>
|
0.503 |
| Average MCC ± 95% Confidence Intervals |
0.720
±
0.059
|
>
|
0.508
±
0.132
|
| Sensitivity |
0.661 |
>
|
0.473 |
| Positive Predictive Value |
0.823 |
>
|
0.543 |
| Total TP |
256 |
>
|
183 |
| Total TN |
44472 |
>
|
44446 |
| Total FP |
62 |
<
|
174 |
| Total FP CONTRA |
33 |
>
|
28 |
| Total FP INCONS |
22 |
<
|
126 |
| Total FP COMP |
7 |
<
|
20 |
| Total FN |
131 |
<
|
204 |
| P-value |
2.22210847902e-08 |
Performance plots
-
Comparison of performance of PETfold_pre2.0(seed) and Alterna. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data
(individual counts for PETfold_pre2.0(seed)
and Alterna).
-
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data
(individual counts for PETfold_pre2.0(seed)
and Alterna).
-
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and Alterna. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data
(individual counts for PETfold_pre2.0(seed)
and Alterna).
Performance of PETfold_pre2.0(seed)
- scored higher in this pairwise comparison
1. Total counts & total scores for PETfold_pre2.0(seed)
| Total Base Pair Counts |
|---|
| Total TP |
256 |
| Total TN |
44472 |
| Total FP |
62 |
| Total FP CONTRA |
33 |
| Total FP INCONS |
22 |
| Total FP COMP |
7 |
| Total FN |
131 |
| Total Scores |
|---|
| MCC |
0.736 |
| Average MCC ± 95% Confidence Intervals |
0.720
±
0.059
|
| Sensitivity |
0.661 |
| Positive Predictive Value |
0.823 |
| Nr of predictions |
18 |
Performance of Alterna
- scored lower in this pairwise comparison
1. Total counts & total scores for Alterna
| Total Base Pair Counts |
|---|
| Total TP |
183 |
| Total TN |
44446 |
| Total FP |
174 |
| Total FP CONTRA |
28 |
| Total FP INCONS |
126 |
| Total FP COMP |
20 |
| Total FN |
204 |
| Total Scores |
|---|
| MCC |
0.503 |
| Average MCC ± 95% Confidence Intervals |
0.508
±
0.132
|
| Sensitivity |
0.473 |
| Positive Predictive Value |
0.543 |
| Nr of predictions |
18 |
Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based
on the paper by Gardener & Giegerich, 2004.
| 
