plw (version 1.30.0)

topRankSummary: 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.

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)