Trying to plot MFI using Flowworkspace but parameters are transformed by 'flowjo_biexp'. How do I get untransformed values?
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mark.brown • 0
@markbrown-16062
Last seen 3.6 years ago

We analyse our data with FlowJo but I am looking to import the workspaces into R to generate graphs and reports for a database. I use the flowworkspace package to do this and have had great success through the vignettes with population statistics but I would also like to graph MFIs. When I look at the intensities they are transformed (Transformer: flowJo_biexp).

 - Should I try to invert this transformation? If so, how?

- Or is the raw data for the compensated parameters available? If so, how do I get to it?

Many thanks,

Mark

flowworkspace • 792 views
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 3 months ago
(Private Address)

See https://github.com/RGLab/flowWorkspace/blob/trunk/R/getStats.R#L28

If that built-in 'pop.MFI' (https://github.com/RGLab/flowWorkspace/blob/trunk/R/getStats.R#L117) somehow doesn't meet your need, you can write you own version and pass it to the generic 'getStats' API

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The pop.quantiles type works, (also with inverse.transform = TRUE) but for some reason the pop.MFI type returns a null data.table (0 rows and 0 cols). Do you know why this might be?

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The built-in versoin ofo 'pop.MFI' only computes the channels with non-NA stains (or desc column in your flowFrame). To remove that restriction, you can simply provide your own version of 'pop.MFI' by deleting that line of code

pd <- pd[!is.na(desc), ]
 
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Thanks a lot for the explanation. All greatly appreciated

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