[BioC] flowFlowJo error

[Gabriel Kaufman]

When I try to read in a FlowJo (version 7.6.1 for Windows) workspace file into R using the flowFlowJo package, I get a bizarre error that does not seem to be previously described. It appears to be from an underlying R syntax call, but I have not found any reference as to how flowFlowJo generates this message. Is this a problem with my workspace, or a difficulty with the package?


I copy the console output below. Note that there is no error traceback available...


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> library(flowFlowJo)
Loading required package: MASS
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
Warning message:
replacing previous import ‘.__C__character’ when loading ‘methods’ 
> FlowJo1 <- readFlowJoList("/Users/kaufman_home/Documents/Mazer lab files/data/Notch-Notch ligand phenotyping/Lung-DCcs-FlowJo.wsp")

Getting a workspace for: Lung-DCcs-FlowJo.wsp... got it!

Having a bit of trouble finding the FCS files, 
Will try:  /Users/kaufman_home/Documents/Mazer lab files/data/Notch-Notch ligand phenotyping .... found them!
Working on:  Lung-DCs_Isotype.fcs  FSC-A, SSC-A subset:Q1: Comp-APC-Cy7-A- , Comp-PerCP-A+  FSC-A, SSC-A subset:Q2: Comp-APC-Cy7-A+ , Comp-PerCP-A+  FSC-A, SSC-A subset:Q3: Comp-APC-Cy7-A+ , Comp-PerCP-A-  FSC-A, SSC-A subset:Q3: Comp-APC-Cy7-A+ , Comp-PerCP-A-:Comp-Alexa Fluor 488-A-Error in gateNodeToFilterObject(gateNode, quiet = TRUE, stripComp = TRUE) : 
  (list) object cannot be coerced to type 'double'
> FlowJo1
Error: object 'FlowJo1' not found
> traceback()
No traceback available 
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] flowFlowJo_1.12.0 MASS_7.3-16      

loaded via a namespace (and not attached):
[1] Biobase_2.14.0  feature_1.2.8   flowCore_1.20.0 graph_1.32.0    ks_1.8.5       
[6] rrcov_1.3-01    stats4_2.14.1   tools_2.14.1    XML_3.9-2      

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Thank you in advance for your help.



Gabriel Kaufman
Meakins-Christie Laboratories
McGill University Health Centre