gistfile1.r

# Start with basic quality controls from lumi, highlight
# samples by tissue information, also extract gender information
colors <- brewer.pal(3, 'Set1')
tissues <- pData(lumiData)$Tissue
gender <- pData(lumiData)$Sex

# Basic sample relations
pdf('sampleRelations_mds_0.1_withRedos.pdf')
plotSampleRelation(lumiData, method='mds', cv.Th=0.1, col=colors[tissues])
dev.off()

pdf('sampleRelations_cluster_0.1_withRedos.pdf')
plotSampleRelation(lumiData, method='cluster', cv.Th=0.1)
dev.off()

# From the vignette. t-test of intensity value differences for probes
# on the X chromosome
mdX <- cmdscale(dist(t(exprs(lumiData)[fData(lumiData)$CHR=='X', ])), 2)

pdf('X_withDuplicates_labels.pdf', width=14, height=14)
plot(mdX, 
     pch=15,
     col=c(rgb(255, 0, 0, 100, maxColorValue=255), 
           rgb(0, 0, 255, 100, maxColorValue=255))[pData(lumiData)$Sex],
     cex=1.2)
text(mdX[, 1], mdX[, 2], labels=pData(lumiData)$SampleLabel, cex=.75)
dev.off()