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
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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
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
--
f?r nur 19,99 Euro/mtl.!* http://portal.gmx.net/de/go/dsl02
Could you point me to the file where this needs to be fixed. I
couldn't grep it in the code.
On 03.07.2009, at 09:18, Bastian Angermann wrote:
> sprintf("0,%d", pData(params)[p, "minRange"])
Sorry, that's in the read.FCS function in IO.R line 144.
-------- Original-Nachricht --------
> Datum: Mon, 6 Jul 2009 12:54:12 -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
> Could you point me to the file where this needs to be fixed. I
> couldn't grep it in the code.
>
>
>
> On 03.07.2009, at 09:18, Bastian Angermann wrote:
>
> > sprintf("0,%d", pData(params)[p, "minRange"])
--
f?r nur 19,99 Euro/mtl.!* http://portal.gmx.net/de/go/dsl02
