RSadvance: Advanced Rank Sum Analysis
In RankProd: Rank Product method for identifying differentially expressed genes with application in meta-analysis

Description Usage Arguments Value Note Author(s) References See Also Examples

The function performs the Rank Sum method to identify differentially expressed genes. It is possible to do either a one-class or two-class analysis. It is also possible to combine data from different studies (e.g. datasets generated by different laboratories. This function has been kept only to guarantee backward compatibility, in fact the same results can be obtained by RankProducts.

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RSadvance(data, cl, origin, num.perm = 100, logged = TRUE, na.rm = TRUE, 
gene.names = NULL, plot = FALSE, rand = NULL, huge = FALSE, fast = TRUE,
tail.time = 0.05)

`data`	the data set that should be analyzed. Every row of this dataset must correspond to a gene
`cl`	a vector containing the class labels of the samples. In the two class unpaired case, the label of a sample is either 0 (e.g., control group) or 1 (e.g., case group). For one class data, the label for each sample should be 1
`origin`	a vector containing the origin labels of the samples. The label is the same for samples within one lab and different for samples from different labs.
`num.perm`	in this version of the package, this parameter is not used any more, but it is kept for backward compatibility
`logged`	if "TRUE" data have been previously log transformed. Otherwise it should be set as "FALSE"
`na.rm`	if "FALSE", the NA value will not be used in computing rank. If "TRUE" (default), the missing values will be replaced by the genewise median of the non-missing values. Gene with a number of missing values greater than 50% are still not considered in the analysis
`gene.names`	if "NULL", no gene name will be attached to the outputs, otherwise it contains the vector of gene names
`plot`	if "TRUE", plot the estimated pfp vs the rank of each gene
`rand`	if specified, the random number generator will be put in a reproducible state
`huge`	if "TRUE" not all the outputs are evaluated in order to save space
`fast`	if "FALSE" the exact p-values for the Rank Sum are evaluated for any size of the dataset. Otherwise (default), if the size of the dataset is too big, only the p-values that can be computed in "tail.time" minutes (starting from the tail) are evaluated with the exact method. The others are estimated with the Gaussian approximation. If calculateProduct="TRUE" this parameter is ignored
`tail.time`	the time (default 0.05 min) dedicated to evaluate the exact p-values for the Rank Sum. If calculateProduct="TRUE" this parameter is ignored

A result of identifying differentially expressed genes between two classes. The identification consists of two parts, the identification of up-regulated and down-regulated genes in class 2 compared to class 1, respectively.

`pfp`	Estimated percentage of false positive predictions (pfp) up to the position of each gene under two identificaiton each
`pval`	Estimated pvalues for each gene being up- and down-regulated
`RSs`	Rank-sum (average rank) of each genes
`RSrank`	Rank of the rank sum of each gene in ascending order
`Orirank`	Ranks in each possible pairing, in this version of the function this is not used to compute rank sum. It is here only for backward compatibility
`AveFC`	Fold change of average expression under class 1 over that under class 2, if multiple origin, than avraged across all origin. Log-fold change if data is in log scaled, original fold change if data is unlogged
`allrank1`	Fold change of class 1/class 2 under each origin. Log-fold change if data is in log scaled
`allrank2`	Fold change of class 2/class 1 under each origin. Log-fold change if data is in log scaled
`nrep`	Total number of replicates considering all the different origins
`groups`	Vector of labels (as cl).

Percentage of false prediction (pfp), in theory, is equivalent of false discovery rate (FDR), and it is possible to be large than 1.

The function looks for up- and down- regulated genes in two seperate steps, thus two pfps are computed and used to identify gene that belong to each group.

The function is able to deal with single or multiple-orgin studies. It is similar to funcion RP.advance expect a rank sum is computed instead of rank product. This method is more sensitive to individual rank values, while rank product is more robust to outliers (refer RankProd vignette for details)

Francesco Del Carratore, francesco.delcarratore@postgrad.manchester.ac.uk
Andris Janckevics, andris.jankevics@gmail.com

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

topGene RP RPadvance plotRP RP.advance RankProducts

#Suppose we want to check the consistence of the data 
#sets generated in two different 
#labs. For example, we would look for genes that were \
# measured to be up-regulated in 
#class 2 at lab 1, but down-regulated in class 2 at lab 2.\
data(arab)
arab.cl2 <- arab.cl

arab.cl2[arab.cl==0 &arab.origin==2] <- 1

arab.cl2[arab.cl==1 &arab.origin==2] <- 0

arab.cl2
##[1] 0 0 0 1 1 1 1 1 0 0


#look for genes differentially expressed
#between hypothetical class 1 and 2
arab.sub=arab[1:500,] ##using subset for fast computation
arab.gnames.sub=arab.gnames[1:500]
Rsum.adv.out <- RSadvance(arab.sub,arab.cl2,arab.origin,
                            num.perm=100,logged=TRUE,
                            gene.names=arab.gnames.sub,rand=123)

attributes(Rsum.adv.out)