fudge2 {siggenes} | R Documentation |
Computes the fudge factor as described by Tusher et al. (2001).
fudge2(r, s, alpha = seq(0, 1, 0.05), include.zero = TRUE)
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 |
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 |
SAM was developed by Tusher et al. (2001).
!!! There is a patent pending for the SAM technology at Stanford University. !!!
Holger Schwender, holger.schw@gmx.de
Tusher, V., Tibshirani, R., and Chu, G. (2001). Significance Analysis of Microarrays Applied to the Ionizing Radiation Response. PNAS, 98, 5116-5121.