Table 1 |
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|
Area under the ROC curve in synthetic data |
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|
Differentially spliced exons |
Noise level σ |
PECA-SI |
RMA-LM |
PLIER-LM |
RMA-SI |
PLIER-SI |
RMA-MIDAS |
PLIER-MIDAS |
FIRMA |
|
|
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|
1 |
0.7 |
0.99 |
0.99 |
0.98 |
0.99 |
0.94 |
0.99 |
0.95 |
0.99 |
|
2 |
0.7 |
0.99 |
0.98 |
0.96 |
0.98 |
0.94 |
0.98 |
0.94 |
0.98 |
|
3 |
0.7 |
0.97 |
0.94 |
0.91 |
0.93 |
0.93 |
0.94 |
0.93 |
0.93 |
|
4 |
0.7 |
0.94 |
0.87 |
0.83 |
0.86 |
0.90 |
0.90 |
0.90 |
0.86 |
|
5 |
0.7 |
0.92 |
0.83 |
0.79 |
0.82 |
0.88 |
0.87 |
0.88 |
0.81 |
|
1 |
1.0 |
0.94 |
0.91 |
0.89 |
0.97 |
0.92 |
0.90 |
0.85 |
0.94 |
|
2 |
1.0 |
0.94 |
0.91 |
0.88 |
0.93 |
0.89 |
0.91 |
0.86 |
0.91 |
|
3 |
1.0 |
0.90 |
0.86 |
0.82 |
0.86 |
0.82 |
0.87 |
0.81 |
0.84 |
|
4 |
1.0 |
0.88 |
0.83 |
0.80 |
0.84 |
0.80 |
0.85 |
0.79 |
0.82 |
|
5 |
1.0 |
0.74 |
0.68 |
0.68 |
0.69 |
0.69 |
0.72 |
0.67 |
0.66 |
|
|
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|
The synthetic data were generated according to Equation 8 at two different noise levels, σ = 0.7 or σ = 1. The first column indicates the number of synthetic differential splicing events generated within a gene. At each combination of the noise level and the number of differentially spliced exons, 1,000 genes were investigated. In each case, the probe-level PECA-SI procedure (see Equation 6) was compared to the standard SI procedures RMA-SI, PLIER-SI, RMA-MIDAS and PLIER-MIDAS, the two-way ANOVA-based approaches RMA-LM and PLIER-LM, and the FIRMA algorithm. The largest area under the curve (AUC) value across the methods is indicated in bold. |
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|
Laajala et al. Genome Biology 2009 10:R77 doi:10.1186/gb-2009-10-7-r77 |
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