[BioC] flowFlowJo error
Gabriel Kaufman
gabriel.kaufman at mail.mcgill.ca
Wed Feb 8 16:37:43 CET 2012
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...
--------------------------------------------------------
> 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
--------------------------------------------------------
Thank you in advance for your help.
Gabriel Kaufman
Meakins-Christie Laboratories
McGill University Health Centre
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