Question: flowQ qaProcess fails to run in both Windows and Mac OS: What am I doing wrong?
6.3 years ago by
Guest User • 12k
Guest User • 12k wrote:
Hi everyone, I am a newcomer to R and Bioconductor. I have been working to set up flow cytometry packages for analysis of data from our instrument. For a native R package, I've installed flowCore, flowQ, flowViz and flowStats libaries, and have been following along with the tutorials (i.e. file:///C:/Program%20Files/R/R-2.15.3/library/flowQ/doc/DataQual ityAssessment.pdf). However, despite best efforts, and trying installs in both Windows and Linux, the qaProcess fails to run in the flowQ library. It looks like there might be a missing library, but frankly I'm stumped as to how to procede. I would greatly appreciate your advice! Jason Here is an example, taken from the flowCore tutorial, where the program fails and generates an error. I have little idea what these errors mean. > library(flowQ) > data(GvHD) > GvHD <- GvHD[1:10] > dest <- file.path(tempdir(), "flowQ") > qp1 <- qaProcess.cellnumber(GvHD, outdir=dest, cFactor=0.75) creating summary plots...Error in if (scaleFac != 1) newDims <- dims * scaleFac : missing value where TRUE/FALSE needed In addition: Warning messages: 1: running command 'C:\Windows\system32\cmd.exe /c identify "C:/Users/ jeriksen/AppData/Local/Temp/RtmpyWMjlk/flowQ/images/rQ2ZMUQHWQ/summary .pdf"' had status 1 2: In .local(.Object, ...) : NAs introduced by coercion -- output of sessionInfo(): R version 2.15.3 (2013-03-01) Platform: x86_64-w64-mingw32/x64 (64-bit) locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  tools grid splines stats graphics grDevices  utils datasets methods base other attached packages:  flowQ_1.18.0 latticeExtra_0.6-24 RColorBrewer_1.0-5  parody_1.16.0 bioDist_1.30.0 KernSmooth_2.23-10  outliers_0.14 flowStats_1.16.0 flowWorkspace_1.4.0  hexbin_1.26.2 IDPmisc_1.1.17 flowViz_1.22.0  XML_3.96-1.1 RBGL_1.34.0 graph_1.36.2  Cairo_1.5-2 cluster_1.14.4 mvoutlier_1.9.9  sgeostat_1.0-25 robCompositions_1.6.3 car_2.0-16  nnet_7.3-6 compositions_1.30-1 energy_1.5.0  MASS_7.3-23 boot_1.3-7 tensorA_0.36  rgl_0.93.935 fda_2.3.4 Matrix_1.0-12  lattice_0.20-15 zoo_1.7-9 flowCore_1.24.2  rrcov_1.3-3 pcaPP_1.9-49 mvtnorm_0.9-9994  robustbase_0.9-7 Biobase_2.18.0 BiocGenerics_0.4.0  BiocInstaller_1.8.3 loaded via a namespace (and not attached):  annotate_1.36.0 AnnotationDbi_1.20.7 DBI_0.2-6  feature_1.2.8 geneplotter_1.36.0 IRanges_1.16.6  ks_1.8.12 parallel_2.15.3 RSQLite_0.11.3  stats4_2.15.3 xtable_1.7-1 -- Sent via the guest posting facility at bioconductor.org.
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