EBAM Analysis Using Wilcoxon Rank Statistics
Description
Generates the required statistics for an Empirical Bayes Analysis of Microarrays analysis using standardized Wilcoxon rank statistics.
Should not be called directly, but via ebam(..., method = wilc.ebam).
Usage
1 2 
Arguments
data 
a matrix or a data frame. Each row of

cl 
a numeric vector of length 
approx50 
if 
ties.method 
either 
use.offset 
should an offset be used in the Poisson regression employed to estimate
the density of the observed Wilcoxon rank sums? If 
df.glm 
integer specifying the degrees of freedom of the natural cubic spline employed in the Poisson regression. 
use.row 
if 
rand 
numeric value. If specified, i.e. not 
Details
Standardized versions of the Wilcoxon rank statistics are computed. This means that W* = (W  mean(W)) / sd(W) is used as expression score z, where W is the usual Wilcoxon rank sum statistic or Wilcoxon signed rank statistic, respectively.
In the computation of these statistics, the ranks of ties are by default set to the minimum rank. In the computation of the Wilcoxon signed rank statistic, zeros are randomly set either to a very small positive or negative value.
If there are less than 50 observations in each of the groups, the exact null distribution
will be used. If there are more than 50 observations in at least one group, the null
distribution will by default be approximated by the standard normal distribution. It is,
however, still possible to compute the exact null distribution by setting approx50
to FALSE
.
Value
A list of statistics required by ebam
.
Author(s)
Holger Schwender, holger.schw@gmx.de
References
Efron, B., Storey, J.D., Tibshirani, R.\ (2001). Microarrays, empirical Bayes methods, and the false discovery rate, Technical Report, Department of Statistics, Stanford University.
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
, wilc.stat