fudge2 {siggenes} | R Documentation

## Fudge Factor

### Description

Computes the fudge factor as described by Tusher et al. (2001).

### Usage

      fudge2(r, s, alpha = seq(0, 1, 0.05), include.zero = TRUE)

### Arguments

`r` | a numeric vector. The numerator of the test statistic computed for each gene is represented by one component of this vector.
`s` | a numeric vector. Each component of this vector corresponds to the denominator of the test statistic of a gene.
`alpha` | a numeric value or vector specifying quantiles of the `s` values. If `alpha` is numeric, this quantile of `s` will be used as fudge factor. Otherwise, the `alpha` quantile of the `s` values is computed that is optimal following the criterion of Tusher et al.\ (2001).
`include.zero` | if `TRUE`, s0=0 is also a possible choice for the fudge factor.

### Value

`s.zero` | the value of the fudge factor s0.
`alpha.hat` | the optimal quantile of the `s` values. If s0=0, `alpha.hat` will not be returned.
`vec.cv` | the vector of the coefficients of variations. Following Tusher et al. (2001), the optimal `alpha` quantile is given by the quantile that leads to the smallest CV of the modified test statistics.
`msg` | a character string summarizing the most important information about the fudge factor.

### Author(s)

Holger Schwender, holger.schw@gmx.de

### References

Tusher, V., Tibshirani, R., and Chu, G. (2001). Significance Analysis of Microarrays Applied to the Ionizing Radiation Response. PNAS, 98, 5116-5121.

### See Also

`SAM-class`,`sam`

[Package siggenes version 1.64.0 Index]