error flowtrans cytof flowFrame
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Entering edit mode
@niklaushurlimann-11103
Last seen 4.9 years ago

I get the following error while trying to apply flowTrans to some cytof flowFrame. Can help me anybody how to proceed further. So far I tested the function with the example described in flowTrans: A Package for Optimizing Data Transfromations for Flow Cytometry. Many thanks

file.in=list.files(path,pattern="*.fcs")
> flowFrame_1<-read.FCSfile.in[[1]])
> colnames(flowFrame_1)
 [1] "Time"         "Event_length" "Y89Di"        "Rh103Di"      "Ag107Di"      "Ag109Di"      "Cd110Di"      "Cd111Di"     
 [9] "Cd112Di"      "In113Di"      "Cd114Di"      "In115Di"      "I127Di"       "Ba137Di"      "Ba138Di"      "La139Di"     
[17] "Ce140Di"      "Pr141Di"      "Nd142Di"      "Nd143Di"      "Nd144Di"      "Nd145Di"      "Nd146Di"      "Sm147Di"     
[25] "Sm148Di"      "Sm149Di"      "Nd150Di"      "Eu151Di"      "Sm152Di"      "Eu153Di"      "Sm154Di"      "Gd155Di"     
[33] "Gd156Di"      "Gd158Di"      "Tb159Di"      "Gd160Di"      "Dy161Di"      "Dy162Di"      "Dy163Di"      "Dy164Di"     
[41] "Ho165Di"      "Er166Di"      "Er167Di"      "Er168Di"      "Tm169Di"      "Er170Di"      "Yb171Di"      "Yb172Di"     
[49] "Yb173Di"      "Yb174Di"      "Lu175Di"      "Yb176Di"      "Pt190Di"      "Ir191Di"      "Pt192Di"      "Ir193Di"     
[57] "Pt194Di"      "Pt195Di"      "Pt196Di"      "Au197Di"      "Pt198Di"      "Pb204Di"      "Pb206Di"      "Pb207Di"     
[65] "Pb208Di"      "Bi209Di"     
> trans<-flowTrans(flowFrame_1, "mclMultivArcSinh",colnames(flowData)[3:66], n2f=FALSE, parameters.only=FALSE)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘flowTrans’ for signature ‘"flowFrame", "character", "NULL", "logical", "logical"’

R version 3.2.3 (2015-12-10)

Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=French_Switzerland.1252  LC_CTYPE=French_Switzerland.1252    LC_MONETARY=French_Switzerland.1252
[4] LC_NUMERIC=C                        LC_TIME=French_Switzerland.1252    

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

other attached packages:
 [1] memisc_0.99.7-1           MASS_7.3-45               ggplot2_2.1.0             openCyto_1.8.4            data.table_1.9.6         
 [6] flowTrans_1.22.0          flowUtils_1.34.0          flowClust_3.8.0           clue_0.3-51               corpcor_1.6.8            
[11] mnormt_1.5-4              ellipse_0.3-8             RBGL_1.46.0               graph_1.48.0              Biobase_2.30.0           
[16] BiocGenerics_0.16.1       flowStats_3.28.1          flowWorkspace_3.16.16     gridExtra_2.2.1           ncdfFlow_2.16.1          
[21] BH_1.60.0-2               RcppArmadillo_0.7.100.3.0 cluster_2.0.4             mvoutlier_2.0.6           sgeostat_1.0-27          
[26] fda_2.4.4                 Matrix_1.2-6              flowViz_1.34.1            lattice_0.20-33           flowCore_1.36.9          
[31] mvtnorm_1.0-5            

loaded via a namespace (and not attached):
 [1] nlme_3.1-128          mcmc_0.9-4            matrixStats_0.50.2    pbkrtest_0.4-6        RColorBrewer_1.1-2   
 [6] Rgraphviz_2.14.0      tools_3.2.3           R6_2.1.2              KernSmooth_2.23-15    DBI_0.4-1            
[11] mgcv_1.8-12           colorspace_1.2-6      nnet_7.3-12           sp_1.2-3              GGally_1.0.1         
[16] chron_2.3-47          quantreg_5.24         SparseM_1.7           sROC_0.1-2            scales_0.4.0         
[21] lmtest_0.9-34         DEoptimR_1.0-4        hexbin_1.27.1         robustbase_0.92-6     stringr_1.0.0        
[26] multicool_0.1-9       minqa_1.2.4           R.utils_2.3.0         MCMCpack_1.3-6        rrcov_1.3-11         
[31] lme4_1.1-12           zoo_1.7-13            jsonlite_0.9.20       gtools_3.5.0          R.oo_1.20.0          
[36] dplyr_0.4.3           car_2.1-2             magrittr_1.5          Rcpp_0.12.5           munsell_0.4.3        
[41] R.methodsS3_1.7.1     stringi_1.1.1         cvTools_0.3.2         zlibbioc_1.16.0       plyr_1.8.3           
[46] grid_3.2.3            misc3d_0.8-4          pls_2.5-0             RUnit_0.4.31          codetools_0.2-14     
[51] stats4_3.2.3          XML_3.98-1.4          latticeExtra_0.6-28   vcd_1.4-1             nloptr_1.0.4         
[56] MatrixModels_0.4-1    VIM_4.4.1             gtable_0.2.0          reshape_0.8.5         assertthat_0.1       
[61] ks_1.10.3             e1071_1.6-7           coda_0.18-1           class_7.3-14          IDPmisc_1.1.17       
[66] pcaPP_1.9-60          robCompositions_2.0.0 rgl_0.95.1441        

 

flowtrans flowcore • 578 views
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Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 6 months ago
(Private Address)

Apparently your "colnames(flowData)[3:66]" is returning NULL instead of a character vector that is expected. Check you 'flowData' to see if it is a valid flowFrame.

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