topRankSummary: Return or plots analysis result for top ranking or selected...
In plw: Probe level Locally moderated Weighted t-tests.

Description Usage Arguments Author(s) See Also Examples

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

1
2
3

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)

`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.

Magnus Astrand

plw

# ------------------------------------------
# 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)