flowFit parentFitting() produces error in integrate() with own data, not exemplary data
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Entering edit mode
@geroknittel-14284
Last seen 7.0 years ago

Hi everybody,

I won't manage to get the flowFit package running (it works with the provided exemplary data though). Even though the parentFitting function does it's job, I can run proliferationFitting neither with a sample file, nor with the exact same file I used as the parent population (available here).

library(flowFit)
library(flowCore)

 

parent <- read.FCS('parentee.fcs', transformation=FALSE) 
parent.fitting <- parentFitting(parent, 'FL7-A')
peak_position  <- parent.fitting@parentPeakPosition
peak_size      <- parent.fitting@parentPeakSize

fitting <- proliferationFitting(parent, 'FL7-A', peak_position, peak_size, verbose = TRUE)

 

This is the output:

parentFitting: No dataRange provided. Setting range from channel range: 999
Setting logDecades using acquisition resolution
proliferationFitting: No logDecades provided. Setting LOG dynamic range from flowFrame: log decades: 3
Estimating generations distance with formulas: 100.242988556106
Binning data into: 1024 breaks
Smoothing data with Kolmogorov-Zurbenko low-pass linear filter.
Loading data from FCS column: FL7-A
Setting parStart and Building model. Estimated number of peaks: 1
FITTING MODEL...
It.    0, RSS =    144.364, Par. =          1    33.1153    9.49543    100.243
It.    1, RSS =    26.7385, Par. =   0.689073    33.1153    9.49543    100.243
It.    2, RSS =    23.8328, Par. =   0.618924    33.1153    9.49543    100.243
It.    3, RSS =    23.8252, Par. =   0.614949    33.1153    9.49543    100.243
It.    4, RSS =    23.8252, Par. =   0.614936    33.1153    9.49543    100.243
It.    5, RSS =    23.8252, Par. =   0.614936    33.1153    9.49543    100.243
It.    6, RSS =    23.8252, Par. =   0.614936    33.1153    9.49543    100.243
It.    7, RSS =    23.8252, Par. =   0.614936    33.1153    9.49543    100.243
Error in integrate(.fx, lower = 0, upper = (fittingdata@dataRange), parSS = .this.generation.pars) :
  evaluation of function gave a result of wrong length

 

I don't really understand what's happening here, no clue on how to fix this. It would be really great if you could help me out.

Best regards from Cologne,
Gero

 

sessionInfo():

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] flowCore_1.42.3 flowFit_1.14.0

loaded via a namespace (and not attached):
 [1] graph_1.54.0        Rcpp_0.12.13        kza_4.0.0           cluster_2.0.6      
 [5] MASS_7.3-47         BiocGenerics_0.22.1 lattice_0.20-35     rrcov_1.4-3        
 [9] pcaPP_1.9-72        caTools_1.17.1      tools_3.4.1         parallel_3.4.1     
[13] grid_3.4.1          Biobase_2.36.2      KernSmooth_2.23-15  latticeExtra_0.6-28
[17] flowViz_1.40.0      corpcor_1.6.9       IDPmisc_1.1.17      gtools_3.5.0       
[21] matrixStats_0.52.2  RColorBrewer_1.1-2  bitops_1.0-6        robustbase_0.92-7  
[25] gdata_2.18.0        compiler_3.4.1      DEoptimR_1.0-8      gplots_3.0.1       
[29] stats4_3.4.1        minpack.lm_1.2-1    mvtnorm_1.0-6       hexbin_1.27.1

 

flowFit parentFitting() integrate() • 806 views
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0
Entering edit mode
@geroknittel-14284
Last seen 7.0 years ago

I would like to close this thread. The problem was simply the FCS file created by FlowJo. Using the original file and gating it in R solves the problem.

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