geneLists: Ordered Gene Lists from 5 microarray studies

In RankAggreg: Weighted Rank Aggregation

Description

This dataset contains five lists of genes, each of size 25, from five independent microarray studies on prostate cancer. The lists are given in Table 4 in the manuscript by DeConde et al. Lists form the rows of the dataset with columns corresponding to the ranks of genes in each individual study.

Usage

data(geneLists)

Format

A matrix of size 5 by 25 containing 5 lists of genes.

Source

R. DeConde, S. Hawley, S. Falcon, N. Clegg, B. Knudsen, and R. Etzioni. Combining results of microarray experiments: a rank aggregation approach. Stat Appl Genet Mol Biol, 5(1):Article15, 2006.

Examples

data(geneLists)
topList <- RankAggreg(geneLists, 5, N=700, seed=100, convIn=3)
plot(topList)

Example output

 Iteration 1 :  Optimal value:  12.4 
 Optimal List:   HPN,AMACR,SLC25A6,GDF15,SAT 

 Iteration 2 :  Optimal value:  12 
 Optimal List:   HPN,AMACR,FASN,GDF15,ATF5 

 Iteration 3 :  Optimal value:  12 
 Optimal List:   HPN,AMACR,FASN,SLC25A6,NME2 

 Iteration 4 :  Optimal value:  12 
 Optimal List:   HPN,AMACR,NME2,SAT,GDF15 

 Iteration 5 :  Optimal value:  11.6 
 Optimal List:   HPN,AMACR,FASN,NME2,GDF15 

 Iteration 6 :  Optimal value:  12 
 Optimal List:   HPN,AMACR,FASN,OGT,NME2 

 Iteration 7 :  Optimal value:  11.6 
 Optimal List:   HPN,AMACR,FASN,GDF15,NME2 

 Iteration 8 :  Optimal value:  11.6 
 Optimal List:   HPN,AMACR,FASN,NME2,GDF15 

 Iteration 9 :  Optimal value:  11.6 
 Optimal List:   HPN,AMACR,FASN,GDF15,NME2 

RankAggreg documentation built on July 8, 2020, 6:20 p.m.