[BioC] flowClust results in subset filters

Kenneth Lo c.lo at stat.ubc.ca
Wed May 6 01:56:28 CEST 2009


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
>



More information about the Bioconductor mailing list