\item{x}{the value returned by function RP, 
RPadvance, RSadvance, RankProducts or RP.advance}

\item{cutoff}{The pfp threshold value used to select genes}

\item{method}{if cutoff is provided, the method needs to be selected to identify 
genes. "pfp" uses percentage of false prediction, which is a default setting.
"pval" uses p-values which is less stringent than pfp}

\item{logged}{if "TRUE", data has been logged, otherwise set it to "FALSE"}

\item{logbase}{base used when taking log, used to restore the fold change.The 
default value is 2, this will be ignored if logged=FALSE}

\item{gene.names}{if "NULL", no gene name will be attached to the output table}

\item{num.gene}{number of candidates genes of interests, if cutoff is provided,
this will be ignored}
Two tables of identified genes with gene.index: index of gene in the original
data set RP/Rsum: Computed rank product/sum for each gene FC:(class1/class2):
Expression Fold change of class 1/ class 2. pfp: estimated pfp for each gene
if the gene is used as cutoff point P.value: estimated p-value for each gene
Table 1 list genes that are up-regulated under class 2, Table 1 ist genes that
are down-regulated under class 2
Indentify diiffentially expressed genes using rank product method
# Load the data of Golub et al. (1999). data(golub)
# contains a 3051x38 gene expression
# matrix called golub, a vector of length called golub.cl
# that consists of the 38 class labels,
# and a matrix called golub.gnames whose third column
# contains the gene names.

#use a subset of data as example, apply the rank
#product method
subset <- c(1:4,28:30)
#Setting rand=123, to make the results reproducible,

#identify genes
RP.out <- RP(golub[,subset],golub.cl[subset],rand=123)

#get two lists of differentially expressed genes
#by setting FDR (false discivery rate) =0.05


#using pvalue<0.05

#by selecting top 10 genes
Fangxin Hong \email{fhong@salk.edu}
Breitling, R., Armengaud, P., Amtmann, A., and Herzyk, P.(2004) Rank Products: A 
simple, yet powerful, new method to detect differentially regulated genes in 
replicated microarray experiments, FEBS Letter, 57383-92
\code{\link{plotRP}} \code{\link{RP}}
\code{\link{RPadvance}} \code{\link{RSadvance}