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Question: Visualization of analysis of multiple cell lines
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gravatar for Alexander Az.
8 weeks ago by
Armenia
Alexander Az.0 wrote:

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?

ThanksĀ in advance,

Alexander

ADD COMMENTlink modified 8 weeks ago by Gordon Smyth35k • written 8 weeks ago by Alexander Az.0
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gravatar for Gordon Smyth
8 weeks ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

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.

ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by Gordon Smyth35k
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