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

[M. Jankowski]

Byron,

This got me back on track! Thank you!

Matt

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.
>
> >
> > The flowSet discussion in the HowTo does cover filtering and gating.
> > When I attempt to read my file in as a flowset I get errors.
> >
> > Section 2.2.1 give the instruction:
> > > frames <- lapply(dir(system.file("extdata", "compdata", "data",
> > +     package = "flowCore"), full.names = TRUE), read.FCS)
> > > as(frames, "flowSet")
>
> When reading from files it is almost always best to use read.flowSet,
> which automates much of this process.
>
> >
> > I'm not certain how to put my "/home/mdj/Rdata/" directory into the
> > context of the system.file function. Here is my best attempt:
> > > frames <= lapply("/home/mdj/data/Rdata/", readFCS)
>
> Your example differs from the example in the How To in two ways.
> First, the lapply() is actually performed on the directory listing.
> For example,
>
> lapply(dir("/home/mdj/data/Rdata",patt="\\.fcs$"),readFCS)
>
> is more likely to do what you want. The inclusion of a pattern ensures
> that only things with the "fcs" extension will be used. However, it
> mostly serves as an example by way of construction so you shouldn't
> need to use it unless you need to do something that read.flowSet
> cannot (like grab the FCS files from URLS or something).
>
> Also, you have <= instead of <-. <= is an inequality. Personally, I
> hate <- with a passion (b[b<-1] = 0. Whoops.) and thus tend to use
> just =, unless it is impossible for some reason (very rarely).
>
> > Error: object "frames" not found
> >
> > When I attempt "read.flowSet":
> >
> > > read.flowSet("/home/mdj/Rdata/")
>
> This is because the first parameter of read.flowSet is actually a
> pattern not a path (I know, the opposite of dir... but this is the way
> things go). This is because you're usually in the same directory as
> your FCS files. You actually want:
>
> read.flowSet(path="/home/mdj/Rdata/")
>
> or something similar.
>
> > These errors have me stumped. I think the organization of this library
> > is quite keen. I like the flowFrame object in what I think of as a
> > flowSet vector (with nice header). Would someone show me how to:
> >
> > 1) gate my data for the 'flowFrame' object and then plot the gated data?
>
> > 2) work my way through creating a flowSet object? I think my main
> > problem is that I am clumsy with the system.file syntax.
> >
> > My apologies if these questions are answered elsewhere. If this is the
> > case please point me in the right direction.
> >
> > Any and all help is appreciated. Thanks!
> >
>
> Hope that helps.
>
> > Matt
> >
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> >
>
>
> --
> Byron Ellis (byron.ellis at gmail.com)
> "Oook" -- The Librarian
>