Hi,

I have a raw gene expression data matrix (data; matrix of 5000 rows [genes] and 100 columns [samples]). I want to take the log2FC distance matrix generated from plotMDS and run that through boot.phylo. I want to do this because I want to take their exact method for calculating log2FC on an abbreviated list of the top 500 genes. The problem appears to be how I am writing out the function step. Any help is appreciated.

Larry

d<-DGEList(data, group=group)

**###Group membership is assigned in a different step. That's not the problem.**

MDS<-plotMDS(d, gene.selection = "common")

**###I want to take the MDS$distance.matrix and take it through boot.phylo.
###The matrix is asymmetrical, so I make it symmetrical first.**

MDSmatrix<-as.data.frame(MDS$distance.matrix)

upper<-t(MDSmatrix)

symmetrical.matrix<-upper + MDSmatrix

matrix<-as.matrix(symmetrical.matrix)

dist.matrix<-as.dist(matrix)

data.nj<-nj(dist.matrix)

**####Now, put this into boot.phylo**

pdf("Tree.pdf")

data.func<- function(x) nj(plotMDS(DGEList(x, group = group))gene.selection="common")

node.prob.1000<-boot.phylo(data.nj, data, data.func, B=1000)

plot(data.nj)

nodelabels(node.prob.1000)

mtext("log2 FC", outer= T, cex = 1.4, font=2)

dev.off()