I have a certain EList containing data for three cell lines. I need to plot MDS plots for each one of them separately. Are there any ideas of how can this be feasible?

plotMDS(EList$E, ...)

would plot an MDS for all 3 cell lines. How can I visualise each one seperately?

Thanks in advance,

Alexander

First, note that you don't need to manage components of the EList object yourself. Just call

plotMDS(EList, ...)

and the function will extract the expression scores automatically.

To plot subsets of samples, just use standard subsetting operations in R. An EList can be manipulated as if it was a matrix. If CellLine is a vector taking values 1, 2 and 3, you could use

plotMDS(Elist[, CellLine==1], ...)

to plot samples of the first cell line. This works because rows of the Elist correspond to genes while columns correspond to samples.