[BioC] flowCore::parameters

[Bastian Angermann]

Hi Florian, 

thanks for the quick reply. I've updated flowCore/Clust to SVN revision 40494/40493.

There is a minor issue with the read.FCS function:

> read.FCS("../data/Yoav/HDM013 V2 1005 NS no.fcs")
Error in sprintf("0,%d", pData(params)[p, "minRange"]) :
  use format %f, %e, %g or %a for numeric objects

I've fixed this by replacing the %d by %g.

Best Bastian
-------- Original-Nachricht --------
> Datum: Thu, 02 Jul 2009 15:55:29 -0700
> Von: Florian Hahne <fhahne at fhcrc.org>
> An: Bastian Angermann <AngerB at gmx.de>
> CC: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] flowCore::parameters

> Hi Bastian,
> I just fixed this issue in the devel branch. Note that you will need to 
> update both flowCore and flowClust. There have been substantial changes 
> to the way things were handled compared to the previous release, so it 
> would be tedious to port this fix back into the release branch.
> 
> In the meantime, evaluating this before calling the parameters method 
> should fix the issue in a sort of hackish way:
> 
> setMethod("parameters",
>           signature=signature(object="filterResult"),
>           definition=function(object)
>           unique(unlist(sapply(filterDetails(object),
>                                function(x) if(is.list(x)) x$parameters))))
> 
> Thanks for reporting the issue,
> Florian
> 
> 
> Bastian Angermann wrote:
> > Hi list,
> >
> > I am having trouble with the parameters method in flowCore. When
> applying parameters to an element of multipleFilterResult generated by a
> tmixFilter, R will throw the following error:
> > Error in x$parameters : $ operator is invalid for atomic vectors
> >
> > This came up while trying to apply an other filter to the result of a
> tmixFilter.
> >
> > Best,
> > Bastian Angermann
> >
> > Here's how to reproduce the error (R 2.9.0 flowCore SVN 39752 /flowClust
> SVN 39598):
> >
> > data(GvHD)
> > fcsData <- GvHD[[1]]
> >
> > tmixGate <- tmixFilter(parameters=c("FSC-H","SSC-H"), K=1)
> >
> > recGate <-
> rectangleGate(.gate=list("FSC-H"=c(0,1000),"SSC-H"=c(0,1000)))
> > rf <- filter(fcsData,recGate)
> > tf <-filter(fcsData,tmixGate %subset% rf )
> >
> >   
> >> tf
> >>     
> > A filterResult produced by the filter named 'tmixFilter in
> defaultRectangleGate'
> >  resulting in multiple populations:
> >          1
> >   
> >> class(tf)
> >>     
> > [1] "multipleFilterResult"
> > attr(,"package")
> > [1] "flowCore"
> >   
> >> parameters(tf)
> >>     
> > [1] "FSC-H" "SSC-H"
> >   
> >> parameters(tf[[1]])
> >>     
> > Error in x$parameters : $ operator is invalid for atomic vectors
> >
> >
> >
> >
> >   
> 
> 
> -- 
> Florian Hahne, PhD
> Computational Biology Program
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> PO Box 19024
> Seattle, Washington 98109-1024
> 206-667-3148
> fhahne at fhcrc.org

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