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

[Nishant Gopalakrishnan]

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
>>>>>
>>>>> _______________________________________________
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>>>>
>>>>
>>>> -- 
>>>> 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
>>
>>
>
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