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
