Trying to plot MFI using Flowworkspace but parameters are transformed by 'flowjo_biexp'. How do I get untransformed values?
1
0
Entering edit mode
mark.brown • 0
@markbrown-16062
Last seen 5.8 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 • 1.8k views
ADD COMMENT
0
Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 2.5 years 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

ADD COMMENT
0
Entering edit mode

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
0
Entering edit mode

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
0
Entering edit mode

Thanks a lot for the explanation. All greatly appreciated

ADD REPLY

Login before adding your answer.

Traffic: 656 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6