Computes the required statistics for an Empirical Bayes Analysis with a modified t- or F-test.

Should not be called directly, but via
`ebam(..., method = z.ebam)`

or `find.a0(..., method = z.find)`

,
respectively.

1 2 3 4 5 6 |

`data` |
a matrix, data frame or ExpressionSet object. Each row of |

`cl` |
a numeric vector of length |

`a0` |
a numeric value specifying the fudge factor. |

`quan.a0` |
a numeric value between 0 and 1 specifying the quantile of the standard deviations of the genes that is used as fudge factor. |

`B` |
an integer indicating how many permutations should be used in the estimation of the null distribution. |

`var.equal` |
should the ordinary t-statistic assuming equal group variances
be computed? If |

`B.more` |
a numeric value. If the number of all possible permutations is smaller
than or equal to (1+ |

`B.max` |
a numeric value. If the number of all possible permutations is smaller
than or equal to |

`n.subset` |
an integer specifying in how many subsets the |

`fast` |
if |

`n.interval` |
the number of intervals used in the logistic regression with
repeated observations for estimating the ratio |

`df.ratio` |
integer specifying the degrees of freedom of the natural cubic spline used in the logistic regression with repeated observations. |

`rand` |
integer. If specified, i.e. not |

A list of object required by `find.a0`

or `ebam`

, respectively.

Holger Schwender, holger.schw@gmx.de

Efron, B., Tibshirani, R., Storey, J.D. and Tusher, V. (2001).
Empirical Bayes Analysis of a Microarray Experiment, *JASA*,
96, 1151-1160.

Schwender, H., Krause, A. and Ickstadt, K. (2003). Comparison of
the Empirical Bayes and the Significance Analysis of Microarrays.
*Technical Report*, SFB 475, University of Dortmund, Germany.

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