Dear all,

I have expression counts from an RNAseq experiment for several libraries. I
now want to use the MDS plot function to visualise similarities of the
expression profiles of the various libraries. Looking at the expression
matrix as well as at the resulting MDS plot, however, I saw some aspects
different to my expectation, so I tested some aspects on a small example,
e.g.:

c<-cbind(a=rep(2,50),b=rep(4,
50),c=rep(8,50),d=rep(8,50) )
d <- DGEList(counts=c)
jpeg(filename="mds-plot_matrix-abcd",width=700,height=700)
plotMDS(d)
dev.off()

c<-cbind(b=rep(4,50),c=rep(8,50),d=rep(8,50),a=rep(2,50) )
d <- DGEList(counts=c)
jpeg(filename="mds-plot_matrix-bcda",width=700,height=700)
plotMDS(d)
dev.off()

With those results, however, I got totally confused:
- why don't identical libraries cluster together?
- why does the positioning of the libraries in the mds plot depend on the
ordering of the columns in the expression matrix?

What did I do wrong here?

Thanks a lot, Lina

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