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

[spyne at broadinstitute.org]

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
>
>