Question

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 6.5 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 • 2.2k views

ADD COMMENT • link updated 6.5 years ago by Jiang, Mike ★ 1.3k • written 6.5 years ago by mark.brown • 0

score 0 · Answer 1 · 2018-06-08

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Jiang, Mike ★ 1.3k

@jiang-mike-4886

Last seen 3.1 years ago

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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

ADD COMMENT • link 6.5 years ago Jiang, Mike ★ 1.3k

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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?

ADD REPLY • link 6.5 years ago mark.brown • 0

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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), ]

ADD REPLY • link 6.5 years ago Jiang, Mike ★ 1.3k

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Thanks a lot for the explanation. All greatly appreciated

ADD REPLY • link 6.5 years ago mark.brown • 0