Measuring Between Array Distances

This will show you if you have any arrays where the median expression levels are very different from one another. This might indicate problems with annealing and reproducibility.


library(genefilter)
dd <- dist2(log2(exprs(raw)))
diag(dd)<-0
dd.row <-as.dendrogram(hclust(as.dist(dd)))
library("latticeExtra")
row.ord <- order.dendrogram(dd.row)
legend <-list(top=list(fun=dendrogramGrob,
args=list(x=dd.row, side="top")))
lp <- levelplot(dd[row.ord,row.ord],
scales=list(cex="0.5", x=list(rot=90)),xlab="",
ylab="", legend=legend)
lp


For my dataset this gave the following output.