Hi Florian, Yeap, I should have updated flowClust, too. I was not aware that the summarizeFilter method needed to be defined in flowClust because of the tmixFilter class. It works perfectly now. Thanks again for the fix. Kenneth On 5-May-09, at 4:36 PM, Florian Hahne wrote: > Hi Kenneth, > did you also update your flowClust? I had to add the summarizeFilter > method there. The version you need is 2.3.1. > When running the last command of the example code I get this > names(filterDetails(fr, "tmixFilter in defaultRectangleGate")) > [1] "filter" "populations" "expName" "varNames" > "K" [6] "w" "mu" "sigma" > "lambda" "nu" [11] "z" "u" > "label" "uncertainty" "ruleOutliers" > [16] "flagOutliers" "rm.min" "rm.max" "logLike" > "BIC" [21] "ICL" > > Those are all the additional slots from the tmixFilterResult class. > > Florian > > Kenneth Lo wrote: >> Hi Florian, >> >> Thanks a lot for the fix, which clearly makes the integration of >> flowClust with flowCore more sense as now it may tell the class >> assignment from tmixFilter when combining its use with other >> filtering/gating operations defined in flowCore. I've just checked >> out the most updated copy from the devel branch (version 1.11.2), >> and tried the example code in your email. The filter method in the >> 2nd last line of the example code does return a >> multipleFilterResult object now, which is what we desire. However, >> similar to Bastian's experience, I could only access the tmixFilter >> object but not the tmixFilterResult object in the filterDetails >> list. Some slots which describe the fitted distribution using >> flowClust, e.g., mu, sigma and lambda, are found in the >> tmixFilterResult class but not in tmixFilter. Are there any means >> to retrieve these pieces of information? >> >> Thanks again, >> >> Kenneth >> >> >> >> >> On 5-May-09, at 11:41 AM, Florian Hahne wrote: >> >>> Hi Bastian, Kenneth, >>> the problem in this case is that flowClust extends the >>> multipleFilterResult class, adding all the mixture parameters and >>> stuff. The subsetFilter operation is defined in flowCore, which >>> doesn't really know about all these additional slots. We do have a >>> mechanism in place to deal with such cases, i.e, the >>> summarizeFilter method which is called whenever a filter is >>> evaluated. This is basically just a hook that has access to both >>> the input filter and the filterResult, and it can be used to add >>> arbitrary items to the filterDetails slot. I added a >>> summarizeFilter method for tmixFilters which does exactly that. >>> The following will still give you a multipleFilterResult object as >>> the result of the subsetFilter operation but now with additional >>> flowClust parameters attached in the filterDetails. >>> >>> library(flowClust) >>> data(GvHD) >>> foo <- GvHD[[1]] >>> rg <- rectangleGate("FSC-H"=c(100,600), "SSC-H"=c(200, 700)) >>> tm <- tmixFilter(parameters=c("FSC-H", "SSC-H"), K=3) >>> fr <- filter(foo, tm %subset% rg) >>> names(filterDetails(fr, "tmixFilter in defaultRectangleGate")) >>> >>> Note that there are three items in the filterDetails list, one for >>> each of the components of the subsetFilter and one for the >>> subsetFilter itself, and that the latter contains copies of values >>> of the former two. This is intentional, albeit a bit unfortunate >>> in this case, since the additional flowClust parameters contain a >>> lot of information (large matrices, indexing vectors...), which is >>> unnecessarily copied here. >>> >>> bw, >>> Florian >>> >>> >>> Bastian Angermann wrote: >>>> Thank you very much and have a great weekend. >>>> >>>> Bastian >>>> >>>> -------- Original-Nachricht -------- >>>> >>>>> Datum: Fri, 01 May 2009 14:16:01 -0700 >>>>> Von: Florian Hahne <fhahne at="" fhcrc.org=""> >>>>> An: Bastian Angermann <angerb at="" gmx.de=""> >>>>> Betreff: Re: [BioC] flowClust results in subset filters >>>>> >>>> >>>> >>>>> Ok, I will take a look asap, >>>>> Florian >>>>> >>>>> Bastian Angermann wrote: >>>>> >>>>>> Hi Florian, >>>>>> >>>>>> I've come over a minor issue with the current return type of a >>>>>> filter operation that subsets a tmix-filter within an other >>>>>> filter. >>>>>> >>>>>> While the current return type of multipleFilterResult allows to >>>>>> access >>>>>> the class assignment by the tmix-Filter, the results describing >>>>>> the fitted distribution (i.e. means, proportions and covariance >>>>>> matrices) are not accessible. The filter included in the >>>>>> >>>>> filterDetails in the appropriate gate is of type tmixFilter and >>>>> not >>>>> tmixFilterResult, which would of course have a redundant subSet. >>>>>> Access to the parameters of the fitted distributions would be >>>>>> quite usefull. >>>>>> >>>>>> Best, >>>>>> Bastian >>>>>> -------- Original-Nachricht -------- >>>>>> >>>>>>> Datum: Mon, 27 Apr 2009 17:41:43 -0700 >>>>>>> Von: Florian Hahne <fhahne at="" fhcrc.org=""> >>>>>>> An: Bastian Angermann <angerb at="" gmx.de=""> >>>>>>> Betreff: Re: [BioC] flowClust results in subset filters >>>>>>> >>>>>> >>>>>>> Hi Bastian, >>>>>>> I just committed the changes to the devel branch of the package >>>>>>> >>>>> (version >>>>>>> 1.11.1). >>>>>>> It might take a day or two to build, but it would be great if >>>>>>> you could >>>>>>> take a look at this version first. I would like to hold off on >>>>>>> bumping things back into release unless we are all happy with >>>>>>> it. >>>>>>> If you know how to build the devel package from source you >>>>>>> should be able to get the 1.11.1 version as of now. >>>>>>> Florian >>>>>>> >>>>>>> Bastian Angermann wrote: >>>>>>> >>>>>>>> Hi Florian, >>>>>>>> >>>>>>>> thanks for your reply. Let me know if I can do any beta >>>>>>>> testing of the new code. >>>>>>>> >>>>>>>> Cheers, >>>>>>>> Bastian. >>>>>>>> -------- Original-Nachricht -------- >>>>>>>> >>>>>>>>> Datum: Sun, 26 Apr 2009 22:49:02 -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] flowClust results in subset filters >>>>>>>>> >>>>>>>> >>>>>>>>> Hi Bastian, >>>>>>>>> this is indeed a feature which wasn't implemented yet. I >>>>>>>>> fixed the code and everything seems to be working as >>>>>>>>> intended now, but I want >>>>>>>>> >>>>> to >>>>>>>>> give it some more rigorous testing before submitting. I am >>>>>>>>> planning >>>>>>>>> >>>>> to >>>>>>>>> push that back into the release branch since it is more of a >>>>>>>>> bug fix than feature addition. >>>>>>>>> If you want to be more independent of the types of comparisons >>>>>>>>> >>>>> between >>>>>>>>> gating steps, you might want to take a look at the workFlow >>>>>>>>> stuff (as >>>>>>>>> >>>>> >>>>>>>>> described in the package vignette). There you can compute >>>>>>>>> summary statistics for a particular gating operation based >>>>>>>>> on another reference view in the workFlow (via the >>>>>>>>> additional 'reference' argument of the summary method) >>>>>>>>> bw, >>>>>>>>> Florian >>>>>>>>> >>>>>>>>> >>>>>>>>> On 24.04.2009, at 10:30, Bastian Angermann wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> I am using R2.9.0 and the 2.4 version of Bioconductor. When >>>>>>>>>> I try to >>>>>>>>>> >>>>> >>>>>>>>>> run >>>>>>>>>> a tmixfilter subsetted on a rectangular gate the result is >>>>>>>>>> of class logicalFilterResult thus I am unable to access the >>>>>>>>>> individual clusters: >>>>>>>>>> ################################################# >>>>>>>>>> library(flowCore) >>>>>>>>>> library(flowClust) >>>>>>>>>> data(rituximab) >>>>>>>>>> >>>>>>>>>> r_filter <- >>>>>>>>>> rectangleGate("FSC.H"=c(100,500),"SSC.H"=c(100,500)) >>>>>>>>>> # gate boundaries are not meant to be meaningful. >>>>>>>>>> t_filter <- tmixFilter("tmix", c("FSC.H", "SSC.H"), K=3) >>>>>>>>>> result <- filter(rituximab,t_filter %subset% r_filter) >>>>>>>>>> >>>>>>>>>> class(result) >>>>>>>>>> ################################################ >>>>>>>>>> >>>>>>>>>> Is that a bug, missing feature or am I missing something? >>>>>>>>>> I'd like to be able to see the result of the >>>>>>>>>> tmixFilter in the context of the ancestor populations, >>>>>>>>>> thus the %subset%. I'am working around that by adding an >>>>>>>>>> index >>>>>>>>>> >>>>> vector >>>>> >>>>>>>>>> to the original flowFrame, to be able to do manual >>>>>>>>>> subsetting, but >>>>>>>>>> it would be nice to to that without this hack. >>>>>>>>>> >>>>>>>>>> Thanks a lot, >>>>>>>>>> Bastian Angermann >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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 >>>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> 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 >>>>>>> >>>>>> >>>>> -- >>>>> 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 >>>>> >>>> >>>> >>> >>> >>> -- >>> 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 >>> >> > > > -- > 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 >