[BioC] flowCore: inverse logicle transformation of flow cytometry data

[spyne at broadinstitute.org]

Hi Nishant,

Thank you very much for the new function and all the other information.

-Pyne


Quoting Nishant Gopalakrishnan <ngopalak at fhcrc.org>:

> Hi Pyne,
>
> I have checked in a method inverseLogicleTransform which you can use to get
> back to the original untransformed data provided you pass in the same
> parameters w,r,d which were used to transform the data initially.  This
> should be available using biocLite("flowCore") tomorrow afternoon.
>
> The default values for the parameters of the logicle transform were obtained
> from the paper by Parks et al. referenced in the man page for the function.
> For detailed information regarding the effect of the change in these
> parameters on the logicle function and how to select optimal parameters for
> your data under consideration, please refer to the paper by Parks et al.
> which goes through the details of selection of the width parameter, dynamic
> range  etc.
>
> Nishant
>
> -----Original Message-----
> From: spyne at broadinstitute.org [mailto:spyne at broadinstitute.org]
> Sent: Tuesday, October 06, 2009 1:15 PM
> To: Nishant Gopalakrishnan
> Subject: Re: [BioC] flowCore: inverse logicle transformation of flow
> cytometry data
>
>
> Hi Nishant,
>
> Thanks a lot for your reply.
>
> The inverse function will be quite helpful for me
> and to many other users who may want to go back to
> the scale they are used to once the analysis is over.
>
> By the way, the logicle function has about 5 parameters,
> I guess. However, I cannot tell this clearly from the
> function description, between w, r, and d, exactly which
> parameter determines the rate of spread of points away
> from zero (origin)? And how was its default value set?
>
> Best regards,
> -Pyne
>
>
> Quoting Nishant Gopalakrishnan <ngopalak at fhcrc.org>:
>
>> Hi Pyne,
>>
>> I am working on a function to calculate the inverse and will be checking
>> in some changes today.
>> Thanks in advance for your patience.
>>
>> Nishant
>>
>> spyne at broadinstitute.org wrote:
>>>
>>> Hi,
>>>
>>> Wondering if the inverse function of logicle was implemented.
>>>
>>> Thanks,
>>> -Pyne
>>>
>>>
>>> Quoting Chao-Jen Wong <cwon2 at fhcrc.org>:
>>>
>>>> Hi, Pyne,
>>>>
>>>> I agree with you that it is good to have an inverse function. Thanks for
>>>> your suggestion and tips. We will try to implement it next week.
>>>>
>>>> Thanks,
>>>> Chao-Jen
>>>>
>>>> spyne at broadinstitute.org wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> The reason I need the inverse function for logicle is because
>>>>> after I have computationally identified the cluster of events in
>>>>> logicle-transformed marker space, now I want to use the knowledge
>>>>> of that range of events in the original, untransformed scale for
>>>>> sorting out similar events in the subsequent experiments.
>>>>>
>>>>> My guess is that this may not be a very far-fetched scenario,
>>>>> and since the transformation is deterministic and bijective
>>>>> anyway, an inverse function would be good to have, at least for
>>>>> the default argument settings. One option is of course a slow
>>>>> numerical computation method.
>>>>>
>>>>> However, since the transformation is monotonic, for a fixed setting
>>>>> of arguments (e.g. the default setting), doing a simple binary search
>>>>> over a reasonable range is a cheap way to approximate the inverse
>>>>> within a desirable accuracy.
>>>>>
>>>>> Thanks!
>>>>> -Pyne
>>>>>
>>>>>
>>>>> Quoting Chao-Jen Wong <cwon2 at fhcrc.org>:
>>>>>
>>>>>> Hi, Pyne
>>>>>>
>>>>>> That is an interesting question. flowCore does not have an inverse
>>>>>> function for the logicle transformation. Since the logicle
>>>>>> transformation is an one-to-one and onto function, it is possible to
>>>>>> implement an inverse function. It is, however, not
>>>>>> straightforward.  Do
>>>>>> you really really need such a function?
>>>>>>
>>>>>> spyne at broadinstitute.org wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I applied logicle transformation (with default arguments)
>>>>>>> to my data points, then detected the subpopulations of
>>>>>>> interest in the transformed data, and now I want to
>>>>>>> revert the subpopulations back to the original scale of
>>>>>>> the untransformed state.
>>>>>>>
>>>>>>> In other words, if I want to apply the inverse of the logicle
>>>>>>> transformtion (applied with default arguments, which I do not
>>>>>>> know) to my data, is that possible?
>>>>>>>
>>>>>>> Thanks.
>>>>>>> -Pyne
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Chao-Jen Wong
>>>>>> Program in Computational Biology
>>>>>> Division of Public Health Sciences
>>>>>> Fred Hutchinson Cancer Research Center
>>>>>> 1100 Fairview Avenue N., M2-B876
>>>>>> PO Box 19024
>>>>>> Seattle, WA 98109
>>>>>> 206.667.4485
>>>>>> cwon2 at fhcrc.org
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Chao-Jen Wong
>>>> Program in Computational Biology
>>>> Division of Public Health Sciences
>>>> Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Avenue N., M2-B876
>>>> PO Box 19024
>>>> Seattle, WA 98109
>>>> 206.667.4485
>>>> cwon2 at fhcrc.org
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>>
>
>
>
>