Why are the numbers different between MAS5.0 analyses in GCOS and EC?
Although the MAS5 algorithm is the same between the Expression Console software and GCOS, the implementation of the algorithm is different. The Expression Console software uses the cross-platform-compatible MAS5 algorithm source code, while the GCOS implementation used Windows-specific libraries. In addition, the development environment and compilers were different between the two software applications resulting in minutely different behavior when dealing with floating point values.
example: A Rat230_2 cel file was analyzed using GCOS and the Expression Console software using absolute analysis. For the p-value there were two observed differences, but these did not affect the detection call.
| Probe Set | EC | GCOS |
|---|---|---|
| 1396753_at | 0.5 | 0.5087891 |
| 1389752_at | 0.09521484 | 0.09960938 |
The signal values differed more, but should have minimal effect on the biological interpretation of the results. The Pearson product moment correlation coefficient is 1.0, and the average difference in signals is 0.0002%. There were four out of the 31099 probe sets that had a > 10% change, but their signal values were all below 60.
| Probe Set | EC | GCOS |
|---|---|---|
| 1393884_at | 1.238289 | 1.684285 |
| 1378478_at | 49.58332 | 56.15875 |
| 1396475_at | 27.01345 | 20.66344 |
| 1393056_at | 1.477951 | 1.105705 |
Further investigation of probe set 1378478_at shows for the 4th probe pair the PM-MM = 0.0000038147 in the GCOS implementation, while it was PM-MM = -0.0000038146973 in the Expression Console software. Since the PM-MM is slightly greater than 0 in the GCOS implementation the contrast value was set to the MM intensity. In the Expression Console software the difference is slightly less than 0 (MM > PM) so the contrast value was set to the PM intensity divided by the typical difference value for the probe set. The resulting contrast values computed were: 27.7534 in GCOS and 21.997242 in the Expression Console software. The remaining probe pairs generated the same contrast values. This one difference resulted in the signal value difference of 49 in the Expression Console software and 56 in GCOS.