gfinak
commented
5 years ago I cannot reproduce your issue:
library(flowCore)
library(flowWorkspace)
#> Loading required package: ncdfFlow
#> Loading required package: RcppArmadillo
#> Loading required package: BH
library(openCyto)
#> Registered S3 method overwritten by 'R.oo':
#> method from
#> throw.default R.methodsS3
f<-list.files(pattern = '1707.*.fcs', path = "~/Downloads/", full.names = TRUE)
flow_Set <- read.flowSet(f)
pDname_subset <- colnames(flow_Set)[4:11]
gS <- GatingSet(flow_Set)
#> .
#> ......done!
trans <- logicleTransform(w = 0.5, t = 262144, m = 4.5, a = 0)
inv <- inverseLogicleTransform(trans = trans)
trans.obj <- flow_trans("logicle", trans, inv, n = 5, equal.space = FALSE)
transList <- transformerList(from = pDname_subset, trans.obj)
gS.t <- transform(gS, transList)
FSC <- "FSC-A,FSC-H"
Singlets = add_pop(gS.t, alias = "Singlets", pop = "+", parent = "root", dims = FSC, gating_method = "singletGate",gating_args = "wider_gate=TRUE,subsample_pct=0.1" )
#> Warning: 'add_pop' is deprecated.
#> Use 'gs_add_gating_method' instead.
#> See help("Deprecated")
#> ...
#> done
getPopStats(gS.t)
#> Warning: '.local' is deprecated.
#> Use 'gs_pop_get_count_fast' instead.
#> See help("Deprecated")
#> name Population Parent Count ParentCount
#> 1: 170718_Tube_001.fcs /Singlets root 10776 10945
#> 2: 170718_Tube_002.fcs /Singlets root 11551 11938
#> 3: 170718_Tube_003.fcs /Singlets root 10838 11187
#> 4: 170718_Tube_004.fcs /Singlets root 10764 11343
#> 5: 170718_Tube_005.fcs /Singlets root 15803 16546
#> 6: 170718_Tube_006.fcs /Singlets root 13838 14622
#> 7: 170718_Tube_007.fcs /Singlets root 13111 13503
sessionInfo()
#> R version 3.6.0 Patched (2019-05-02 r76454)
#> Platform: x86_64-apple-darwin16.7.0 (64-bit)
#> Running under: macOS Sierra 10.12.6
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] parallel stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] openCyto_1.23.2 flowWorkspace_3.33.1
#> [3] ncdfFlow_2.31.3 BH_1.69.0-1
#> [5] RcppArmadillo_0.9.600.4.0 flowCore_1.51.7
#>
#> loaded via a namespace (and not attached):
#> [1] mclust_5.4.5 Rcpp_1.0.1 mvtnorm_1.0-11
#> [4] lattice_0.20-38 corpcor_1.6.9 gtools_3.8.1
#> [7] assertthat_0.2.1 digest_0.6.20 plyr_1.8.4
#> [10] R6_2.4.0 stats4_3.6.0 pcaPP_1.9-73
#> [13] ellipse_0.4.1 evaluate_0.14 highr_0.8
#> [16] pillar_1.4.2 zlibbioc_1.29.0 rlang_0.4.0
#> [19] data.table_1.12.2 Rgraphviz_2.27.0 hexbin_1.27.3
#> [22] R.utils_2.9.0 R.oo_1.22.0 Matrix_1.2-17
#> [25] rmarkdown_1.14 splines_3.6.0 stringr_1.4.0
#> [28] munsell_0.5.0 compiler_3.6.0 xfun_0.8
#> [31] pkgconfig_2.0.2 BiocGenerics_0.29.2 mnormt_1.5-5
#> [34] IDPmisc_1.1.19 htmltools_0.3.6 tidyselect_0.2.5
#> [37] tibble_2.1.3 gridExtra_2.3 matrixStats_0.54.0
#> [40] flowViz_1.47.4 rrcov_1.4-7 crayon_1.3.4
#> [43] dplyr_0.8.3 MASS_7.3-51.4 R.methodsS3_1.7.1
#> [46] grid_3.6.0 RBGL_1.59.8 gtable_0.3.0
#> [49] magrittr_1.5 flowStats_3.43.8 scales_1.0.0
#> [52] graph_1.61.1 RcppParallel_4.4.3 KernSmooth_2.23-15
#> [55] stringi_1.4.4 latticeExtra_0.6-28 robustbase_0.93-5
#> [58] RColorBrewer_1.1-2 tools_3.6.0 Biobase_2.43.1
#> [61] glue_1.3.1 DEoptimR_1.0-8 purrr_0.3.2
#> [64] ks_1.11.5 yaml_2.2.0 clue_0.3-57
#> [67] colorspace_1.4-1 cluster_2.1.0 flowClust_3.21.4
#> [70] fda_2.4.8 knitr_1.23Created on 2019-07-24 by the reprex package (v0.3.0)
There is an argument to singletGate in flowStats named maxit which is set to 5.
Let's start by seeing what version of R and the flow tools you are using (show your sessionInfo()), and then we'll see if we can settle on reproducibility of this bug report, then whether a fix is needed.
Created on 2019-07-24 by the reprex package (v0.3.0)
abbatidanilo
Hello, I am trying to execute a singlet gate with the following commands:
The two dimensions in the FCS variable are of course FSC-A and FCS-H accordingly with the correct dimensions in the flowSet. Please notice than the following command:
behaves normally with no error. It returns (for the every flowFrame - here only the first is reported):
_flowFrame object 'clean_p1_10p2_5sample1.fcs' with 8481 cells and 13 observables: name desc range minRange maxRange $P1 FSC-A FSC-A 262144 0.0000000 262144 $P2 FSC-H FSC-H 262144 0.0000000 262144 $P3 SSC-A SSC-A 262144 0.0000000 262144 $P4 FITC-A CD3 262144 0.0000000 262144 $P5 PE-A CD95 262144 0.0000000 262144 $P6 PerCP-A 7AAD 262144 0.0000000 262144 $P7 PE-Cy7-A CD45Ra 262144 0.0000000 262144 $P8 APC-A CD62L 262144 -0.1038134 262144 $P9 APC-Cy7-A CD8 262144 0.0000000 262144 $P10 Pacific Blue-A CD4 262144 0.0000000 262144 $P11 BV510-A BV510-A 262144 0.0000000 262144 $P12 Time Time 262144 0.0000000 262144 $P13 density density 4713 0.0000000 4712 198 keywords are stored in the 'description' slot
In any case I uploaded the .zip with all the flowFrame used I get the following error:
_Error: (converted from warning) Error in: failed at perc0.2dfF_sample1.fcs
Error in rlm.default(x, y, weights, method = method, wt.method = wt.method, :
(converted from warning) 'rlm' failed to converge in 5 steps
I also tried a simpler version without the latest two parameters:
but I got the same error
Is there any way to overcome this behavior? Please tell me if you need any other element for your analysis
thank you cheers
ori.zip