[BioC] pca plot for gene expression

[Michael Love]

You might get more feedback if you describe what kind of experiment
you have performed (microarray or RNA-Seq?).

The other reason you might not be getting response is that the
principal component functions are not implemented in Bioconductor, but
in base R. So it's not necessarily a Bioconductor question, but a
statistics/R question.

The very basic code for making a PCA plot from an expression set 'e' would be

pc = prcomp( t ( exprs( e ) ) )
plot( pc$x[ , 1:2 ] )

On Tue, Jul 15, 2014 at 8:36 AM, karthik [guest] <guest at bioconductor.org> wrote:
> Hi all,
>
>         I am writing this mail for second time. I wanted perform a pca analysis ,for each  cancer type and genes of interest expression. I just wanted to plot only a single  point which is able represent each cancer and their genes expression .Can you please explain me on it.( And cancer per gene basis should i take median or mean values to represent their expression). Thanks in advance.
>
>
>  -- output of sessionInfo():
>
> pca()
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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