How do I apply a singleParameterTransform to a number of parameters in a flowFrame like the standard transforms?
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@josephhanson-17103
Last seen 3.1 years ago

Hello, I am new to R and flowCore but have been able to figure out most elements of the package that I need. 

However I need to apply a hyperlog transform to a number of parameters in my flowFrame and I can't seem to figure out how that is done correctly.

Currently I am applying a standard log transform in the following way:

 

f <- read.FCS('MyFile.fcs', transformation =FALSE)
f_trans <- transform(f,
                           `Param_02-CD14`=log(`Param_02-CD14`),
                           `Param_03-CD193`=log(`Param_03-CD193`),
                           `Param_05-CD123`=log(`Param_05-CD123`),
                           `Param_11-CD45`=log(`Param_11-CD45`),
                           `Param_12-SSC`=log(`Param_12-SSC`),
                           )

 

This works well for visualizing my data but the analysis that I am replicating is in hyperlog so the data doesn't visually perfectly match up. Also doing the log transform produces some NaNs in my data which breaks the flowDensity function I am attempting to to utilize 'notSubFrame'. For both reasons I would like to try and apply hyperlog transform to the flowFrame but given that this is a singleParameterTransform, the only way I have seen it used is with the eval method which returns the matrix of the single column. 

 

Is there some way to perform the transform and then update the flowFrame object with this transformed data or is there another way this should be used?

 

Thanks in advance for your help!

flowcore flow cytometry flowdensity hyperlog transformation • 397 views
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 14 days ago
(Private Address)

You should use logicle transformation. See details and example codes by typing

?estimateLogicle
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