siggenes (version 1.46.0)

fudge2: 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.

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