9 months ago by
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
First, note that you don't need to manage components of the EList object yourself. Just call
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.