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
