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MAS5Baseline |
| Input | |
| CDF file | The name of the CDF file for experiment set. |
| CEL directory | The name of the directory where all *.cel files can be found. |
| Experiment list file | File with experiment list and their description included into calculation. |
| Baseline experiment | Baseline experiment index. |
| Output | |
| Result | File with the resulting gene expression data in SelTag format. |
| Options | |
| Signal Only | If this flag set on, only signal values will be at the output. Otherwise, detection and detection p-values will be reported also. |
| Background floor | The percent of lowest intencity probes to be considered as background (MAS 5.0 default=2). |
| Zone number | Number of zones (K parameter) in background noise estimation. Default value for MAS 5.0 is 16. |
| Background smooth | The background weight smooth parameter (MAS 5.0 default=100). |
| Target signal | Target value for signal scaling (MAS 5.0 default =500). |
| Normalization factor | Normalization factor (default=1, i.e. the normalization factor is determined automatically). |
| Gamma1Low | Gamma1Low Parameter (MAS5.0 default is equal to Gamma1High = 0.0025). |
| Gamma1High | Gamma1High Parameter (MAS5.0 default is equal to Gamma1Low = 0.0025). |
| Gamma2Low | Gamma2Low Parameter (MAS5.0 default is equal to Gamma2High = 0.003). |
| Gamma2High | Gamma2High Parameter (MAS5.0 default is equal to Gamma2Low = 0.003). |