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$PnE based rescaling is not heeded #16

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xiamaz opened this issue May 23, 2018 · 2 comments
Open

$PnE based rescaling is not heeded #16

xiamaz opened this issue May 23, 2018 · 2 comments

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@xiamaz
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xiamaz commented May 23, 2018

According to the FCS 3.1 specification (and probably older ones, too), logarithmic data channels can be saved in linearized form with $PnE specifying the logarithmic range and minimal value.

Currently the library does not transform these values into logarithmic form for later transformations.

@eyurtsev
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Feel free to file a PR if you know how to fix this

My only concern would be to provide the user with enough information to know that a transformation has been applied to the data

@bpteague
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bpteague commented Jun 29, 2018

Hi @xiamaz - for what it's worth, I've just implemented this functionality in my project, cytoflow, which builds on fcsparser. It's a pretty straightforward transformation to do once you've sucked the data in with fcsparser -- see commit cytoflow/cytoflow@039f9ab for details.

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