openCyto - flowclust.2d throws errors
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@ulrik-stervbo-1723
Last seen 5.6 years ago
Germany

Hello everyone,

I have problems getting the flowClust.2d to work.

library(flowViz)
library(openCyto)

data(GvHD)
fr <- GvHD[[2]]
trs <- logTransform()

fr_trans <- transform(fr, `FL1-H` = trs(`FL1-H`),  `FL2-H` = trs(`FL2-H`))
fr_trans
fres <- flowClust.2d(fr = fr_trans, xChannel = "FL1-H", yChannel = "FL2-H", K = 2, target = c(3,2)) 

gives the error:

Error in validObject(.Object) : 
  invalid class “flowClust” object: 1: invalid object for slot "w" in class "flowClust": got class "NULL", should be or extend class "vector"
invalid class “flowClust” object: 2: invalid object for slot "mu" in class "flowClust": got class "NULL", should be or extend class "matrix"
invalid class “flowClust” object: 3: invalid object for slot "sigma" in class "flowClust": got class "NULL", should be or extend class "array"

which apparently is related to incorrect channel name (https://github.com/RGLab/openCyto/issues/93). However, I fail to see what I am doing wrong.

The example above is taken from flowcore/flowviz filter

Does anyone have any ideas?

 

Thanks,

Ulrik

opencyto flow cytometry • 1.1k views
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> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 15.10

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8     LC_MONETARY=de_DE.UTF-8   
 [6] LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] openCyto_1.8.4            flowWorkspace_3.16.15     gridExtra_2.2.1           ncdfFlow_2.16.1           BH_1.60.0-1               RcppArmadillo_0.6.600.4.0
[7] flowViz_1.34.1            lattice_0.20-33           flowCore_1.36.9          

loaded via a namespace (and not attached):
 [1] nlme_3.1-127          mcmc_0.9-4            matrixStats_0.50.1    pbkrtest_0.4-6        RColorBrewer_1.1-2    Rgraphviz_2.14.0      tools_3.2.5          
 [8] R6_2.1.2              KernSmooth_2.23-15    DBI_0.3.1             BiocGenerics_0.16.1   mgcv_1.8-12           colorspace_1.2-6      nnet_7.3-12          
[15] sp_1.2-2              GGally_1.0.1          chron_2.3-47          sgeostat_1.0-27       graph_1.48.0          quantreg_5.21         Biobase_2.30.0       
[22] flowClust_3.8.0       SparseM_1.7           sROC_0.1-2            flowStats_3.28.1      scales_0.4.0          lmtest_0.9-34         DEoptimR_1.0-4       
[29] hexbin_1.27.1         mvtnorm_1.0-5         robustbase_0.92-5     RBGL_1.46.0           stringr_1.0.0         multicool_0.1-9       minqa_1.2.4          
[36] R.utils_2.2.0         MCMCpack_1.3-5        rrcov_1.3-11          lme4_1.1-11           zoo_1.7-12            jsonlite_0.9.19       gtools_3.5.0         
[43] dplyr_0.4.3           car_2.1-2             R.oo_1.20.0           magrittr_1.5          Matrix_1.2-5          Rcpp_0.12.4           munsell_0.4.3        
[50] R.methodsS3_1.7.1     stringi_1.0-1         cvTools_0.3.2         MASS_7.3-45           zlibbioc_1.16.0       plyr_1.8.3            grid_3.2.5           
[57] misc3d_0.8-4          parallel_3.2.5        pls_2.5-0             splines_3.2.5         RUnit_0.4.31          fda_2.4.4             corpcor_1.6.8        
[64] codetools_0.2-14      stats4_3.2.5          XML_3.98-1.4          latticeExtra_0.6-28   data.table_1.9.6      vcd_1.4-1             nloptr_1.0.4         
[71] MatrixModels_0.4-1    VIM_4.4.1             gtable_0.2.0          clue_0.3-51           reshape_0.8.5         assertthat_0.1        ks_1.10.2            
[78] ggplot2_2.1.0         e1071_1.6-7           coda_0.18-1           flowUtils_1.34.0      class_7.3-14          IDPmisc_1.1.17        pcaPP_1.9-60         
[85] robCompositions_2.0.0 mvoutlier_2.0.6       cluster_2.0.4         rgl_0.95.1441       
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 8 weeks ago
(Private Address)

It was a bug, which has been fixed in the devel branch and will be merged to the latest release as BioC 3.3 is going to be released soon.

Meanwhile, the workaround is to manually load parallel package by `library(parallel)` before `flowClust.2d` call.

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bmuchmore • 0
@bmuchmore-10639
Last seen 5.6 years ago

I am getting the same error even after updating R and Bioconductor to 3.3

Also, before I get the error I am running flowclust.2d on 3 other populations, and I seemingly get no errors.

-Brian Muchmore

 

Gating for 'ldg'
The prior specification has no effect when usePrior=no
Using the parallel (multicore) version of flowClust with 1 cores
Error: failed at Panel_1_32141752_IRCCS_CANTOII_17NOV2015_17NOV2015.fcs _norm.fcs _comp.fcs
Error in validObject(.Object) :
  invalid class "flowClust" object: 1: invalid object for slot "w" in class "flowClust": got class "NULL", should be or extend class "vector"
invalid class "flowClust" object: 2: invalid object for slot "mu" in class "flowClust": got class "NULL", should be or extend class "matrix"
invalid class "flowClust" object: 3: invalid object for slot "sigma" in class "flowClust": got class "NULL", should be or extend class "array"

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
[1] C

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

other attached packages:
 [1] RGtk2Extras_0.6.1         RGtk2_2.20.31            
 [3] doParallel_1.0.10         iterators_1.0.8          
 [5] foreach_1.4.3             flowDensity_1.6.0        
 [7] openCyto_1.10.0           flowWorkspace_3.18.0     
 [9] gridExtra_2.2.1           ncdfFlow_2.18.0          
[11] BH_1.60.0-1               RcppArmadillo_0.6.700.3.0
[13] flowViz_1.36.0            lattice_0.20-33          
[15] flowCore_1.38.0         

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If you've already loaded parallel package, then it could be something else. Without a reproducible example, I can't tell you more about the causes.

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Yeah, I loaded parallel, and it still threw an error. I was mainly just checking to see if the bug fix had been pushed yet or not. Oddly, by moving the location of the flowclust.2d call in the csv file fixed the problem...or it was something else I did without realizing. Speaking of which, could the error possibly be related to having zero cells present when gating? I ask because the error was only being thrown on a rare cell population.

-Brian

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