Table 9.
Comparing t-test results for the three different imputation methods
| Normalization 2 Missing replaced by = -17.28 Log transformed (100% of identified spots picked up) | Normalization 2 Missing replaced by Random sample of minimum from 15 gels in each group Log transformed (91% of identified spots picked up) | Normalization 2 Minimum replaced by Random sample of minimum from all 30 gels Log transformed (91% of identified spots picked up) |
| SSP 1134 | SSP1134 | SSP 1134 |
| SSP 1509 | SSP 1509 | SSP 1509 |
| SSP 1733 | SSP 1733 | SSP 1733 |
| SSP 2309 | SSP 2309 | SSP 2309 |
| SSP 3219 | ||
| SSP 3806 | SSP 3806 | SSP 3806 |
| SSP 4203 | SSP 4203 | SSP 4203 |
| SSP 4225 | SSP 4225 | SSP 4225 |
| SSP 4435 | SSP 4435 | SSP 4435 |
| SSP 4724 | SSP 4724 | SSP 4724 |
| SSP 5413 | SSP 5413 | |
| SSP 6205 | SSP 6205 | SSP 6205 |
| SSP 6304 | SSP 6228 | SSP 6228 |
| SSP 6314 | SSP 6304 | SSP 6304 |
| SSP 6314 | SSP 6314 | |
| SSP 6452 | SSP 6452 | SSP 6452 |
| SSP 7223 | SSP 7223 | SSP 7223 |
| SSP 7334 | SSP 7334 | |
| SSP 7750 | SSP 7750 | SSP 7750 |
In column 1 missing values were replaced with the lowest intensity value in experiment; in column 2 values to replace missing intensities were randomly chosen from the 15 lowest intensity values within a treatment group; in values to replace missing intensities were randomly chosen from the 30 lowest intensity values without regard to treatment group.