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Question: qaProcess.timeline() - error - Unable to find file
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gravatar for lloyd.izard
4 months ago by
lloyd.izard20
lloyd.izard20 wrote:

Good evening ladies and gents,

I am totally new to FCM data analysis and I am facing an error I don't understand.
I have attached my very simple code below : 

##### Script #####
##### remove graph / clear variable and console
graphics.off()
rm(list = ls())
cat('\f')

##### Library + folder #####
wd <- getwd()
setwd(wd)

library("flowCore")
library("flowViz")
library("flowQ")

##### getting the data
ffiles <- list.files(path=".", pattern = ".fcs")
fset <- read.flowSet(ffiles, path=".")
fframe1 <- exprs(fset[[1]])
fframe2 <- exprs(fset[[2]])

# transformation
fset.trans <- transform("FSC-H" = asinh, "SSC-H" = asinh,
                        "FL1-H" = asinh, "FL2-H" = asinh,
                        "FL3-H" = asinh) %on% fset

# quality control
dest <- tempdir()
qp1 <- qaProcess.timeline(fset.trans, channel = "FL1-H", outdir = dest, cutoff = 1)

If you run my code, you might encounter the same error as me. Could you then explain what I got wrong here ?

 

The error is the following : 

________

creating summary plots....ParamŠtre non valide - 240x240
Error in .local(.Object, ...) : 
  Unable to find file 'C:/Users/Lloyd/AppData/Local/Temp/Rtmp0g7AWz/images/FqgEtkNPVu/summary.pdf'
In addition: Warning message:
running command 'convert  -density 240x240 +append C:/Users/Lloyd/AppData/Local/Temp/Rtmp0g7AWz/images/FqgEtkNPVu/summary_1.pdf C:/Users/Lloyd/AppData/Local/Temp/Rtmp0g7AWz/images/FqgEtkNPVu/summary.pdf' had status 4 

________

I understood that the error has to do with the outdir parameter, but I can't figure out what's wrong.

 

sessionInfo() ->

R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252    LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
[5] LC_TIME=French_France.1252    

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

other attached packages:
 [1] flowQ_1.38.0        latticeExtra_0.6-28 RColorBrewer_1.1-2  parody_1.36.0       bioDist_1.50.0      KernSmooth_2.23-15 
 [7] Biobase_2.38.0      mvoutlier_2.0.8     sgeostat_1.0-27     outliers_0.14       BiocGenerics_0.24.0 flowViz_1.42.0     
[13] lattice_0.20-35     flowCore_1.44.1    

loaded via a namespace (and not attached):
 [1] bit64_0.9-7           splines_3.4.3         sp_1.2-6              stats4_3.4.3          blob_1.1.0           
 [6] robustbase_0.92-8     RSQLite_2.0           pillar_1.0.1          VIM_4.7.0             quantreg_5.34        
[11] digest_0.6.13         minqa_1.2.4           colorspace_1.3-2      Matrix_1.2-12         plyr_1.8.4           
[16] pcaPP_1.9-72.1        XML_3.98-1.9          SparseM_1.77          xtable_1.8-2          corpcor_1.6.9        
[21] mvtnorm_1.0-6         scales_0.5.0          lme4_1.1-15           MatrixModels_0.4-1    tibble_1.4.1         
[26] annotate_1.56.1       mgcv_1.8-22           IRanges_2.12.0        car_2.1-6             ggplot2_2.2.1        
[31] nnet_7.3-12           hexbin_1.27.1         lazyeval_0.2.1        pbkrtest_0.4-7        IDPmisc_1.1.17       
[36] mclust_5.4            memoise_1.1.0         GGally_1.3.2          laeken_0.4.6          nlme_3.1-131         
[41] MASS_7.3-48           class_7.3-14          graph_1.56.0          data.table_1.10.4-3   matrixStats_0.52.2   
[46] trimcluster_0.1-2     S4Vectors_0.16.0      kernlab_0.9-25        munsell_0.4.3         cluster_2.0.6        
[51] AnnotationDbi_1.40.0  fpc_2.1-10            pls_2.6-0             compiler_3.4.3        e1071_1.6-8          
[56] vcd_1.4-4             rlang_0.1.6           grid_3.4.3            RCurl_1.95-4.10       nloptr_1.0.4         
[61] cvTools_0.3.2         bitops_1.0-6          boot_1.3-20           gtable_0.2.0          DBI_0.7              
[66] flexmix_2.3-14        reshape_0.8.7         rrcov_1.4-3           robCompositions_2.0.6 zoo_1.8-1            
[71] prabclus_2.2-6        bit_1.1-12            sROC_0.1-2            modeltools_0.2-21     Rcpp_0.12.14         
[76] geneplotter_1.56.0    DEoptimR_1.0-8        diptest_0.75-7        lmtest_0.9-35   


Thank you in advance.

Best regards,
Lloyd

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