sam.wilc {siggenes} | R Documentation |
Performs a Significance Analysis of Microarrays for a set of integer thresholds Delta. Instead of the modified t statistics, it uses Wilcoxon Rank Sums.
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)
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. |
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.
For further analyses with sam.plot
, the results of sam.wilc
must be assigned
to an object.
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.G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response, PNAS, 98, 5116-5121.
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.