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Question: FlowJo workspace cannot be parsed with flowworkspace
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gravatar for vonskopnik
12 weeks ago by
vonskopnik10
vonskopnik10 wrote:

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  

 

ADD COMMENTlink modified 12 weeks ago by Jiang, Mike1.2k • written 12 weeks ago by vonskopnik10
2
gravatar for Jiang, Mike
12 weeks ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:

It didn't find the fcs files, try to specify the path to the fcs files through `path` argument

ADD COMMENTlink written 12 weeks ago by Jiang, Mike1.2k

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 ...

ADD REPLYlink written 12 weeks ago by vonskopnik10

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

ADD REPLYlink written 12 weeks ago by Jiang, Mike1.2k
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