Question

openCyto - flowclust.2d throws errors

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Ulrik Stervbo ▴ 30

@ulrik-stervbo-1723

Last seen 8.0 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 • 1.8k views

ADD COMMENT • link updated 8.0 years ago by bmuchmore • 0 • written 8.0 years ago by Ulrik Stervbo ▴ 30

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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

ADD REPLY • link 8.0 years ago Ulrik Stervbo ▴ 30

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bmuchmore • 0

@bmuchmore-10639

Last seen 8.0 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

ADD COMMENT • link 8.0 years ago bmuchmore • 0

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Entering edit mode

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.

ADD REPLY • link 8.0 years ago Jiang, Mike ★ 1.3k

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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

ADD REPLY • link 8.0 years ago bmuchmore • 0

score 1 · Accepted Answer · 2016-04-25

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Jiang, Mike ★ 1.3k

@jiang-mike-4886

Last seen 2.5 years 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.

ADD COMMENT • link 8.0 years ago Jiang, Mike ★ 1.3k