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ms-leipzig
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@ms-leipzig-15909
Last seen 5.9 years ago
hallo,
just started using R + flowCore to analyze FCS-files. In the "flowCore: data structures package for flow cytometry data" - tutorial at page 22 in section 5.2 i found the following example-snippet:
library(flowWorkspace)
fcsfiles <- list.files(pattern = "CytoTrol"
, system.file("extdata", package = "flowWorkspaceData")
, full = TRUE)
fs <- read.flowSet(fcsfiles)
If I run this in GStudio I get the following error:
> fcsfiles <- list.files(pattern = "CytoTrol"
+ , system.file("extdata", package = "flowWorkspaceData")
+ , full = TRUE)
> fs <- read.flowSet(fcsfiles)
Error in frameList[isFrame] : invalid subscript type 'list'
>
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flowWorkspace_3.28.1 ncdfFlow_2.26.0 BH_1.66.0-1 RcppArmadillo_0.8.500.0 flowCore_1.46.1
loaded via a namespace (and not attached):
[1] pcaPP_1.9-73 Rcpp_0.12.17 plyr_1.8.4 pillar_1.2.2 DEoptimR_1.0-8 compiler_3.5.0
[7] RColorBrewer_1.1-2 bindr_0.1.1 tools_3.5.0 zlibbioc_1.26.0 gtable_0.2.0 tibble_1.4.2
[13] lattice_0.20-35 pkgconfig_2.0.1 rlang_0.2.0 graph_1.57.1 Rgraphviz_2.24.0 parallel_3.5.0
[19] mvtnorm_1.0-7 hexbin_1.27.2 bindrcpp_0.2.2 gridExtra_2.3 stringr_1.3.1 dplyr_0.7.5
[25] cluster_2.0.7-1 IDPmisc_1.1.17 tidyselect_0.2.4 stats4_3.5.0 grid_3.5.0 robustbase_0.93-0
[31] glue_1.2.0 Biobase_2.40.0 data.table_1.11.2 rrcov_1.4-3 R6_2.2.2 XML_3.98-1.11
[37] latticeExtra_0.6-28 purrr_0.2.4 corpcor_1.6.9 magrittr_1.5 scales_0.5.0 matrixStats_0.53.1
[43] MASS_7.3-49 BiocGenerics_0.26.0 assertthat_0.2.0 colorspace_1.3-2 KernSmooth_2.23-15 stringi_1.1.7
[49] flowViz_1.44.0 munsell_0.4.3
Searching in the web I found some comments like "a sub of a vector is a vector again ...". but this doesnt explain this for me.
thanks and best regards
Simon
Hi,
Your
sessionInfo()sounds up to date (at least the same as mine). Next time, please do add missing information as a comment of your original question.In order to track the error, you should check the content of
fcsfilesor simply run the following commandlist.files(pattern = "CytoTrol", system.file("extdata", package = "flowWorkspaceData"), full = TRUE)If you got an empty list, something went wrong during your installation of flowworkspace
If you got file names, check that those files are readable by use of your Windows Explorer (I don't mean Internet Explorer)
If it's still OK, my final guess is that the file path contains characters such as umlaut that R may not like.
If so, copy the FCS files to another folder (
C:\tempfor example) and try again the example code using that directory, that is, replacesystem.file("extdata", package = "flowWorkspaceData")with"C:/temp".Be careful with / and \
HTH
Probably you haven't installed flowWorkspaceData package.