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)