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. |
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. |
Alpha 1 | Alpha 1 parameter for MAS 5.0 algorithm (MAS5.0 default is 0.04). |
Alpha 2 | Alpha 2 parameter for MAS 5.0 algorithm (MAS5.0 default is 0.06). |
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). |
Tau | Tau parameter (MAS5.0 default is 0.015) |