Hello Community,
my standard procedure of parsing a FlowJo workspace has failed for unknown reason. Well, there is an error message but don't why it pops up, since I am doing everything similar to previous analyses. I have used another FlowCytometer this time but this should not be a problem I guess.
After defining my gates (gating tree is equal within the group that I want to parse) I save the wsp-file and try to load it into R:
wsp <- openWorkspace(...)
gs <- parseWorkspace(wsp)
Then I select the group of samples I want to import and get these errors:
Parsing 0 samples
windows version of flowJo workspace recognized.
version X
Error in .addGatingHierarchies(gs, pd, execute, isNcdf, wsType = wsType, :
no sample to be added to GatingSet!
In addition: Warning message:
In .parse.pData(obj = obj, keywords = keywords, sg = sg, keywords.source = keywords.source, :
Multiple FCS files are matched to these samples:
204217.fcs_30205
(i) I don't know what's wrong with the GatingHierarchies (first error). What can I try to overcome this error?
(ii) Multiple FCS files matched to these samples ...
When I run getSamples(wsp) it actually looks like as if this name is unique within my FCS files, so I do not understand this error.
> getSamples(wsp)
sampleID name count pop.counts
1 22 204052.fcs 67714 10
2 23 204054.fcs 66447 10
3 24 204050.fcs 65340 10
4 25 204238.fcs 30888 5
5 26 204038.fcs 2403 4
6 27 204036.fcs 4752 4
7 28 204048.fcs 5000 5
8 29 204044.fcs 1431 2
9 30 204042.fcs 3402 4
10 31 204046.fcs 5000 4
11 10 204205.fcs 31796 10
12 32 204040.fcs 2565 4
13 11 204186.fcs 66764 10
14 12 204199.fcs 54446 10
15 13 204097.fcs 32729 10
16 14 204099.fcs 33545 10
17 15 204101.fcs 32543 10
18 16 204093.fcs 49032 10
19 17 204095.fcs 73413 10
20 18 204078.fcs 43639 10
21 19 204056.fcs 32186 10
22 1 204215.fcs 30602 10
23 2 204217.fcs 30205 10
24 3 204209.fcs 44874 10
25 4 204211.fcs 41139 10
26 5 204213.fcs 30123 10
27 6 204186.fcs 47651 10
28 7 204207.fcs 33000 10
29 8 204201.fcs 60174 10
30 9 204203.fcs 34009 10
31 20 204058.fcs 31069 10
32 21 204060.fcs 30300 10
(Samples with with less than 10 Populations are Compensation files and are not within the group which I want to import.)
Thanks for any suggestions.
Chris
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bindrcpp_0.2.2 flowAI_1.10.1 forcats_0.3.0 stringr_1.3.1 dplyr_0.7.6 purrr_0.2.5 readr_1.1.1 tidyr_0.8.1
[9] tibble_1.4.2 ggplot2_3.0.0 tidyverse_1.2.1 flowWorkspace_3.28.2 ncdfFlow_2.26.0 BH_1.66.0-1 RcppArmadillo_0.9.100.5.0 flowCore_1.46.2
loaded via a namespace (and not attached):
[1] fgsea_1.6.0 colorspace_1.3-2 ggridges_0.5.0 rprojroot_1.3-2 qvalue_2.12.0 corpcor_1.6.9 rstudioapi_0.7 hexbin_1.27.2 IDPmisc_1.1.17
[10] ggrepel_0.8.0 bit64_0.9-7 AnnotationDbi_1.42.1 mvtnorm_1.0-8 lubridate_1.7.4 xml2_1.2.0 splines_3.5.1 GOSemSim_2.6.2 robustbase_0.93-2
[19] knitr_1.20 jsonlite_1.5 broom_0.5.0 cluster_2.0.7-1 GO.db_3.6.0 graph_1.58.0 ggforce_0.1.3 graphite_1.26.1 rrcov_1.4-4
[28] compiler_3.5.1 httr_1.3.1 rvcheck_0.1.0 backports_1.1.2 assertthat_0.2.0 Matrix_1.2-14 lazyeval_0.2.1 cli_1.0.0 tweenr_0.1.5
[37] htmltools_0.3.6 tools_3.5.1 igraph_1.2.2 gtable_0.2.0 glue_1.3.0 reshape2_1.4.3 DO.db_2.9 rappdirs_0.3.1 fastmatch_1.1-0
[46] Rcpp_0.12.18 enrichplot_1.0.2 Biobase_2.40.0 cellranger_1.1.0 nlme_3.1-137 changepoint_2.2.2 ggraph_1.0.2 rvest_0.3.2 clusterProfiler_3.8.1
[55] XML_3.98-1.16 DOSE_3.6.1 DEoptimR_1.0-8 zoo_1.8-4 MASS_7.3-50 zlibbioc_1.26.0 scales_1.0.0 reactome.db_1.64.0 hms_0.4.2
[64] parallel_3.5.1 RColorBrewer_1.1-2 yaml_2.2.0 memoise_1.1.0 gridExtra_2.3 UpSetR_1.3.3 latticeExtra_0.6-28 stringi_1.2.4 RSQLite_2.1.1
[73] S4Vectors_0.18.3 pcaPP_1.9-73 ReactomePA_1.24.0 checkmate_1.8.5 BiocGenerics_0.26.0 BiocParallel_1.14.2 flowViz_1.44.0 rlang_0.2.2 pkgconfig_2.0.2
[82] matrixStats_0.54.0 evaluate_0.11 lattice_0.20-35 bindr_0.1.1 cowplot_0.9.3 bit_1.1-14 tidyselect_0.2.4 plyr_1.8.4 magrittr_1.5
[91] R6_2.2.2 IRanges_2.14.11 DBI_1.0.0 withr_2.1.2 pillar_1.3.0 haven_1.1.2 units_0.6-0 modelr_0.1.2 crayon_1.3.4
[100] KernSmooth_2.23-15 rmarkdown_1.10 viridis_0.5.1 readxl_1.1.0 grid_3.5.1 data.table_1.11.4 blob_1.1.1 Rgraphviz_2.24.0 digest_0.6.17
[109] stats4_3.5.1 munsell_0.5.0 viridisLite_0.3.0
Thank you very much Mike. That worked for me! Unfortunately, now another error pops up while parsing the Workspace:
Creating ncdfFlowSet...
All FCS files have the same following channels:
Time
FSC-A
SSC-A
b-LP502 530/30-E-A
PE-A
b-LP655 LP670-B-A
b-LP735 780/60-A-A
r-660/20-C-A
r-LP685 720/30-A-A
v-450/50-B-A
v-LP502 510/50-A-A
done!
loading data: ... (I cleared that line)
Compensating
gating ...
Error in .cpp_gating(gs@pointer, mat, guid, gains, nodeInd, recompute, :
v-450_50-B-A not found in flowData!
Such question was asked before: Opencyto - detector name not found in flow data, but pretty sure it's there
I noticed a discrepancy in the channelnames: v-450/50-B-A vs. v-450_50-B-A (slash vs. underscore). In another workspace this discrepancy was no problem. What's additionally different to that other workspace is that I entered channel descriptions this time. But that's probably not the problem?! What's also different is that the v-450 channel is compensated this time.
These are my humble suggestions ...
see my response here A: Opencyto - detector name not found in flow data, but pretty sure it's there, which may also explain your error