z.ebam {siggenes} | R Documentation

## EBAM analysis Using t- or F-test

### Description

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.

### Usage

      z.ebam(data, cl, a0 = NULL, quan.a0 = NULL, B = 100, var.equal = FALSE,
          B.more = 0.1, B.max = 30000, n.subset = 10, fast = FALSE,
          n.interval = 139, df.ratio = NULL, rand = NA)

      z.find(data, cl, B = 100, var.equal = FALSE, B.more = 0.1,
          B.max = 30000)

### Arguments

`data` | a matrix, data frame or ExpressionSet object. Each row of `data` (or `exprs(data)`) must correspond to a variable (e.g., a gene), and each column to a sample (i.e.\ observation).
`cl` | a numeric vector of length `ncol(data)` containing the class labels of the samples. For details on how `cl` should be specified, see `ebam`.
`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 `FALSE` (default), Welch's t-statistic will be computed.
`B.more` | a numeric value. If the number of all possible permutations is smaller than or equal to (1+`B.more`)*`B`, full permutation will be done. Otherwise, `B` permutations are used. This avoids that `B` permutations will be used – and not all permutations – if the number of all possible permutations is just a little larger than `B`.
`B.max` | a numeric value. If the number of all possible permutations is smaller than or equal to `B.max`, `B` randomly selected permutations will be used in the computation of the null distribution. Otherwise, `B` random draws of the group labels are used. In the latter way of permuting, it is possible that some of the permutations are used more than once.
`n.subset` | an integer specifying in how many subsets the `B` permutations should be split when computing the permuted test scores. Note that the meaning of `n.subset` differs between the SAM and the EBAM functions.
`fast` | if `FALSE` the exact number of permuted test scores that are more extreme than a particular observed test score is computed for each of the genes. If `TRUE`, a crude estimate of this number is used.
`n.interval` | the number of intervals used in the logistic regression with repeated observations for estimating the ratio f0/f.
`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 `NA`, the random number generator will be set into a reproducible state.

### Value

A list of object required by `find.a0` or `ebam`, respectively.

### Author(s)

Holger Schwender, holger.schw@gmx.de

### References

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.

### See Also

`ebam`, `find.a0`, `d.stat`

[Package siggenes version 1.58.0 Index]