Table 6.
Classification performance of estimated isoform expressions on three experiments
| Experiment | Task | Kallisto | Kallisto (bias) | Salmon | Salmon (bias) | eXpress | eXpress (bias) | RSEM | RSEM (bias) | BaseEM | IntMTQ |
|---|---|---|---|---|---|---|---|---|---|---|---|
| SVM | |||||||||||
| E1 | OV | 0.626(0.101) | 0.606(0.099) | 0.631(0.101) | 0.662(0.100) | 0.624(0.091) | 0.605(0.096) | 0.631(0.097) | 0.648(0.098) | 0.628(0.100) | 0.691(0.090) |
| OV+BRCA | 0.607(0.086) | 0.598(0.085) | 0.572(0.085) | 0.573(0.087) | 0.634(0.082) | 0.604(0.083) | 0.595(0.087) | 0.596(0.084) | 0.551(0.083) | 0.562(0.082) | |
| E2 | OV | 0.643(0.153) | 0.637(0.151) | 0.611(0.152) | 0.648(0.150) | 0.621(0.146) | 0.612(0.149) | 0.595(0.149) | 0.613(0.145) | 0.594(0.143) | 0.660(0.145) |
| OV+BRCA | 0.852(0.072) | 0.851(0.070) | 0.856(0.071) | 0.893(0.062) | 0.852(0.073) | 0.863(0.072) | 0.862(0.068) | 0.869(0.068) | 0.855(0.072) | 0.881(0.055) | |
| E3 | OV | 0.533(0.135) | 0.543(0.134) | 0.540(0.126) | 0.596(0.139) | 0.534(0.130) | 0.558(0.137) | 0.524(0.128) | 0.546(0.133) | 0.532(0.140) | 0.608(0.140) |
| Random Forest | |||||||||||
| OV+BRCA | 0.643(0.120) | 0.721(0.113) | 0.644(0.123) | 0.695(0.110) | 0.655(0.116) | 0.672(0.118) | 0.671(0.122) | 0.672(0.112) | 0.767(0.103) | 0.779(0.095) | |
| E1 | OV | 0.701(0.092) | 0.706(0.089) | 0.717(0.090) | 0.724(0.087) | 0.734(0.091) | 0.744(0.089) | 0.712(0.091) | 0.707(0.094) | 0.719(0.092) | 0.763(0.080) |
| OV+BRCA | 0.628(0.088) | 0.648(0.090) | 0.632(0.091) | 0.664(0.090) | 0.660(0.090) | 0.663(0.092) | 0.622(0.090) | 0.636(0.091) | 0.650(0.087) | 0.660(0.086) | |
| E2 | OV | 0.686(0.134) | 0.685(0.135) | 0.624(0.143) | 0.627(0.144) | 0.616(0.146) | 0.633(0.140) | 0.690(0.135) | 0.693(0.132) | 0.698(0.131) | 0.717(0.130) |
| OV+BRCA | 0.804(0.090) | 0.798(0.090) | 0.721(0.111) | 0.742(0.106) | 0.728(0.109) | 0.729(0.105) | 0.803(0.094) | 0.807(0.095) | 0.799(0.088) | 0.851(0.079) | |
| E3 | OV | 0.540(0.152) | 0.542(0.149) | 0.591(0.147) | 0.632(0.145) | 0.582(0.152) | 0.592(0.147) | 0.569(0.150) | 0.569(0.153) | 0.576(0.148) | 0.628(0.144) |
| OV+BRCA | 0.639(0.117) | 0.638(0.111) | 0.664(0.112) | 0.671(0.112) | 0.686(0.115) | 0.689(0.111) | 0.641(0.115) | 0.648(0.114) | 0.680(0.114) | 0.694(0.111) | |
Note: The mean AUC scores (standard deviation in parentheses) of classifying cell lines by estimated transcript expression in 1000 repeats for each experiment are reported. The best AUCs across the ten methods are bold.