Error biexponential transform flowTrans
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@peterrubbens-11606
Last seen 4.7 years ago

Using the package flowTrans to a flowFrame, I get the following error: 

Error in .Call("biexponential_transform", y, a, b, c, d, f, w, .Machine$double.eps^0.25,  : 
  "biexponential_transform" not available for .Call() for package "flowCore"
Error in p.ab$convergence : $ operator is invalid for atomic vectors. 

How do I solve this? 

flowtrans flow cytometry flowcore • 800 views
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 6 months ago
(Private Address)

The fix is in the latest github https://github.com/RGLab/flowTrans

try devtools::install_github("RGLab/flowTrans", ref = "trunk")

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Thanks, this seems to fix the error (in a number of cases). However, sometimes I get the following error: 

Error in optim(par = p.ab, mclMultivBiexpAB, y = y, c = p.cd[1], d = p.cd[2],  : 
  L-BFGS-B needs finite values of 'fn'

Is this due to the fcs-files? 

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Can you share the reproducible example?

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devtools::install_github("RGLab/flowTrans", ref = "trunk")

library(flowCore)

library(flowTrans)

path = "Desktop/directory/fcsfiles"

filenames = list.files(path)

flowData <- read.flowSet(path = path, transformation = FALSE, pattern = ".fcs")

flowframe <- flowData[[1]]
colnames <- colnames(flowframe)

flowframTrans <- flowTrans(flowframe,'mclMultivBiexp',colnames[1:30], n2f=FALSE, parameters.only = FALSE)

 

I can forward (or share) you an example of an fcs-file as well if you want to. 

 

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you can post it as attachment to the github issue or email to wjiang2@fhcrc.org

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Or can it be due to the fact that in the example above the scatter and fluorescence variables are all optimalized in the same run, whereas in the paper they are treated separately? 

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