[BioC] MDS in edgeR

[Susanne Franssen]

Dear all / authors of the edgeR package,

I have a question concerning the use of the multidimensional scaling
plot provided by the edgeR package.

I have RNA-seq data for 8 libraries from a 2x2 factorial design and I
want produce a mds plot (plotMDS.DGEList) to get a better idea of the
distances between the libraries.
The function plotMDS.DGEList now offers me the option top. Here, I can
choose the x (top=x) genes that show the highest tagwise dispersion
looking at all libraries.

My question is now, what I should consider for the choice of x?
As I have a 2x2 factorial design I was going to choose x=number of all
genes as I don't see a rational for choosing a specific number smaller
number, which would seem somehow arbitrary to me.

Are there any opinions on that?

Thanks a lot,
Susanne