The reset command restores the parameter values after fitting to the default value set by "guess" or to the user-defined default.
The default value, set in init_quad, is 0, i.e., the boundaries must not depend on the external momenta.
The output of the PSI-BLAST program divides the various hits into two categories, i.e. sequences producing significant alignment versus those where the E values are worse than the threshold (default value set at.005).
As the number of publications associated with a gene could vary and we aim for equal representation of each gene, we define the number of documents as a parameter in our method with the default value set to 50.
For interactions of order 2, MDR will examine all possible two-factor combinations among P covariates, (x p1, x p2), 1 ≤ p1, p2 ≤ P. For these two factors, each combination cell is characterized as high or low risk, depending on whether the ratio of cases to controls exceeds a certain threshold with a default value set to 1 (Hans et al. 2003).
The number of permutations was set at 999; all other arguments used the default values set in the function.
Veoh preselects the software parameters for the process from a range of default values set by the thirdparty software…ButVeoh does not itself actively participate or supervise the uploading of files.
The parameters of other methods are selected as their default values set by the authors.
All the other parameters are determined by the default values set by the calls to defaultpar and standardhuman.
The parameters of the simulation algorithms were chosen to have the default values set by the creators of the tool.
Additional TIFF file analysis, data normalization, clustering, and principle components analysis was performed using the Spotfinder, MIDAS and MultiExperiment Viewer Software from The Institute for Genomic Research TIGRRockvillelle, MD, [ 44], [ 12]) and used default values set in the MCW Practical Guide to TIGR Software Use (M. Datta, unpublished).
