[BioC] Help with flowCore Package: Working through the HowTo

[Deepayan Sarkar]

On 6/18/07, Byron Ellis <byron.ellis at gmail.com> wrote:
> On 6/18/07, M. Jankowski <mjankowski at gmail.com> wrote:
> > Hi all,
> >
> >
> > As you can see, I have some pretty far outliers in all the data sets.
> > What procedure would I follow to gate the data to less than 800 for
> > "FSC.H" and "SSC.H"? Further, how would I plot the result of the gated
> > data? In the context of the HowTo I would call my question "2.1.4:
> > Gating and Plotting a flowFrame"
>
> Section 4 of the How To is entirely about filtering/gating with 4.3
> being the section relevant to your question. In your case you probably
> want a rectangleGate of some sort. For example,
>
> Subset(x,rectangleGate("FSC.H"=c(0,800),"SSC.H"=c(0,800)))
>
> would cut your frame down to size. As for plotting, this is somewhat
> more difficult. The flowViz package has some facilities for plotting a
> gate onto a plot of the data, but you'd have to ask Deepayan about
> that---I've never actually used it.

Yes, flowViz does have some utilities for gates, but they didn't make
it to BioC 2.0. You can get the development version from

http://bioconductor.org/packages/2.1/bioc/html/flowViz.html

(which also has a vignette), and it should work with 2.0 if you are
lucky. It may not work with the current devel version of flowCore
though.

-Deepayan