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Download "clean" FCS files #19

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whitews opened this issue Jun 19, 2015 · 4 comments
Closed

Download "clean" FCS files #19

whitews opened this issue Jun 19, 2015 · 4 comments
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@whitews
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whitews commented Jun 19, 2015

Implement downloading of FCS files with ReFlow channel annotations. This allows a project user to export all the files with a common set of channel names. Also, create a file name convention for the "clean" files that is consistent and contains useful metadata about the file such as the site code, subject code, etc.

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whitews commented Jun 24, 2015

1b91c58 closes #19

@whitews whitews closed this as completed Jun 24, 2015
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whitews commented Jun 25, 2015

Need to add the original compensation matrix, if present, to the cleaned FCS file. This is usually stored in the $SPILL metadata key/value.

@whitews whitews reopened this Jun 25, 2015
@whitews whitews self-assigned this Jun 25, 2015
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whitews commented Jun 25, 2015

Added original spillover matrix in 1c4e697

But, the $PnR values need to be set differently to match the original files. A lot of cytometers use 262144 for this value. I'll calculate the max value and set all $PnR values to 262144 if the true max is below that value. If the true value is above, I'll use the real max value.

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whitews commented Jun 26, 2015

feature completed in 424718e

@whitews whitews closed this as completed Jun 26, 2015
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