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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 plots. 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Byron Ellis (byron.ellis at gmail.com) "Oook" -- The Librarian