topRankSummary {plw} | R Documentation

## Return or plots analysis result for top ranking or selected probe sets

### Description

Returns (or plots) t-statistic and/or log2FC for each probe and median for each probe set. P

### Usage

    plotSummaryLog2FC(model,nGenes=50,genesOfRank=1:nGenes,genes=NULL)
    plotSummaryT(model,nGenes=50,genesOfRank=1:nGenes,genes=NULL)
    topRankSummary(model,nGenes=50,genesOfRank=1:nGenes,genes=NULL)

### Arguments

`model` | On object obtained from the function plw.
`nGenes` | Gives summary for the nGenes top ranking genes
`genesOfRank` | Gives summary for genes ranked genesOfRank
`genes` | Gives summary for specific genes.

### Author(s)

Magnus Astrand

### See Also

plw

### Examples

    # ------------------------------------------
    # Example using the result of the analysis of
    # the 6 arrays in the AffySpikeU95Subset data set

    # Loading the data
    data(AffySpikeU95Subset)

    # Defining design and contrast matrix
    group<-factor(rep(1:2,each=3))
    design<-model.matrix(~group-1)
    contrast<-matrix(c(1,-1),1,2)

    # Analyzing using plw
    model1<-plw(AffySpikeU95Subset,design=design,contrast=contrast,
                epsilon=0.01)

    ## Selecting top genes
    topRankSummary(model1,nGenes=10)

    ## Plotting t-statistics and log2FC for top genes
    par(mfrow=c(1,2))
    plotSummaryT(model1,nGenes=20)
    plotSummaryLog2FC(model1,nGenes=20)

[Package plw version 1.4.0 Index]