| topRankSummary {plw} | R Documentation |
Returns (or plots) t-statistic and/or log2FC for each probe and median for each probe set. P
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)