[BioC] Column names in FCS files

Byron Ellis byron.ellis at gmail.com
Wed Jun 20 02:13:07 CEST 2007

You haven't said to what package you're using (if using flowCore,
putting that somewhere in the email will ensure it gets flagged for me
to see).

At the moment you must use the channel names to address parameters in
all flowCore operations---there are a couple of reasons for this, but
the strongest is the simple practical fact that the channel names are
generally unique whereas the marker names are not (nor does the marker
necessarily remain constant within a flowSet).

If all you want are the names and you can deal with using channel
names for constructing gates and the like, you can access the marker
names themselves from a flowFrame by using the featureNames()
function. Note that this does not work at the flowSet reason (though
perhaps it should return a matrix of marker names).

Now, if you REALLY REALLY want to change the channel names to be
marker names you can edit the parameters slot of a flowFrame directly.
It's just an AnnotatedDataFrame with a name and a desc column. The
name column is the channel name and the desc column is the marker name
(if any). You could just swap the two for all rows of desc where
!is.na(desc) or something like that. To do that to a flowSet you
should first convert the set to a list (using as()) and then convert
it back since you'll be mightily confusing flowSet's internal
consistency checking by trying to do it in place. This is, of course,
a Use At Your Own Risk sort of thing...

As far as plotting goes, you can specify a character vector as the 'y'
argument of plot(). If it has a single channel plot() will draw a
histogram, with two channels you get the usual smoothed scatterplot.
Using the flowViz package you can get some more control over your

On 6/19/07, Steven Wanyee <swanyee at gmail.com> wrote:
> I have read a flowset, generated summaries and plotted. The first plot FSC
> versus SSC is pretty straightforward but subsequently, I want to use marker
> names especially when I gate but I cannot seem to be be able to access the
> marker names mapped onto the channel names (i.e FL1-H, FL2-H, FL3-H and
> FL4-H). How do I access those column names?
> --
> Regards,
> ~Steven Wanyee Macharia~
>         [[alternative HTML version deleted]]
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Byron Ellis (byron.ellis at gmail.com)
"Oook" -- The Librarian

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