sam.wilc {siggenes}R Documentation

SAM Analysis using Wilcoxon Rank Sums

Description

Performs a Significance Analysis of Microarrays for a set of integer thresholds Delta. Instead of the modified t statistics, it uses Wilcoxon Rank Sums.

Usage

    sam.wilc(data,x,y,paired=FALSE,na.rm=FALSE,zero.rand=TRUE,rand=NA,use.weights=TRUE,
    delta=1:max(abs(W.diff)),graphic=TRUE,pty.square=TRUE,
    thres=round(quantile(2:max(abs(W.diff)),(0:3)/3)),use.numbers=TRUE,
    helplines=TRUE)

Arguments

data the data set that should be analyzed. Every row of this data set must correspond to a gene.
x vector of the columns of the data set that correspond to the treatment group. In the paired case, (x[i],y[i]) build a pair. If, e.g., the first n1 columns of data contain the gene expression values of the treatment group, x=1:n1.
y vector of the columns of the data set that correspond to the control group. In the paired case, (x[i], y[i]) are an observation pair.
paired paired (TRUE) or unpaired (FALSE) data. Default is FALSE.
na.rm if FALSE (default), the expression scores W of genes with one or more missing values will be set to NA. If TRUE, the missing values will be replaced by the genewise mean of the non-missing values.
zero.rand if TRUE (default), the sign of each Zero in the calculation of the Wilcoxon signed rank score will be randomly assigned. If FALSE, the sign of the Zeroes will be set to '–'.
rand if specified (i.e. not NA), the random number generator will be put in a reproducible state.
use.weights if T (default), then the data points are weighed by 1-λ in the fit of a natural cubic spline.
delta a vector of integer for which the SAM-Wilc analysis should be performed.
graphic if TRUE (default), both the SAM plot and the plots of Delta vs. FDR and Delta vs. number of significant genes are generated. To avoid this plotting, set graphic=FALSE.
pty.square if TRUE (default), a square SAM plot will be generated with x and y axes having the same range.
thres a vector of integer values for Delta for which two lines parallel to the 45-degree line are generated.
use.numbers if TRUE (default), the symbol for each point in the SAM Plot of a SAM-Wilc analysis will be the number of observations that correspond to this point.
helplines if TRUE (default), help lines will be generated in both the Delta vs. FDR and the Delta vs. number of significant genes plot.

Value

a table of statistics (estimate for p0, number of significant genes, number of falsely called genes and FDR) for the specified set of Deltas, a SAM Plot, a Delta vs. FDR plot, and a plot of Delta vs. the number of significant genes.

Note

For further analyses with sam.plot, the results of sam.wilc must be assigned to an object.

Author(s)

Holger Schwender, holger.schw@gmx.de

References

Schwender, H. (2003). Assessing the False Discovery Rate in a Statistical Analysis of Gene Expression Data, Chapter 6, Diploma thesis, Department of Statistics, University of Dortmund, http://de.geocities.com/holgerschw/thesis.pdf.

See Also

sam.plot sam


[Package Contents]