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

[Byron Ellis]

Actually it probably works in devel as well, I haven't committed the
big changeset yet---sidetracked by paper deadlines and WWDC.

On 6/18/07, Deepayan Sarkar <deepayan.sarkar at gmail.com> wrote:
> 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
>


-- 
Byron Ellis (byron.ellis at gmail.com)
"Oook" -- The Librarian