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

spyne at broadinstitute.org spyne at broadinstitute.org
Thu Sep 17 02:29:47 CEST 2009


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.


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

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