Question: Trying to plot MFI using Flowworkspace but parameters are transformed by 'flowjo_biexp'. How do I get untransformed values?
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gravatar for mark.brown
17 months ago by
mark.brown0
mark.brown0 wrote:

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 • 301 views
ADD COMMENTlink modified 17 months ago by Jiang, Mike1.2k • written 17 months ago by mark.brown0
Answer: Trying to plot MFI using Flowworkspace but parameters are transformed by 'flowjo
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gravatar for Jiang, Mike
17 months ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

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 COMMENTlink written 17 months ago by Jiang, Mike1.2k

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 REPLYlink written 17 months ago by mark.brown0

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 REPLYlink written 17 months ago by Jiang, Mike1.2k

Thanks a lot for the explanation. All greatly appreciated

ADD REPLYlink written 17 months ago by mark.brown0
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