Question: Problem parsing data with parseWorkspace
0
gravatar for jokup101
18 days ago by
jokup1010
jokup1010 wrote:

When I try to parse .wsp workspace data I get the following Error:

Error in .cpp_gating(gs@pointer, mat, guid, gains, nodeInd, recompute, : ellipsoidGate::transforming can’t find transformation for FL 4 Log

Loading the workspace seems to work fine and all samples can be loaded via the flowCore package with no issues. Is there something that needs to be changed inside of FlowJo (it seems to be a gating issue) to make it work with the flowWorkspace package?

> ws

FlowJo Workspace Version 1.61 File location: . File name: workspaceTest.wsp Workspace is open.

Groups in Workspace Name Num.Samples 1 All Samples 58

> parseWorkspace(ws)

Choose which group of samples to import:

1: All Samples

Auswahl: 1 |=======================================================================================================|100% ~0 s remaining Parsing 58 samples windows version of flowJo workspace recognized. Creating ncdfFlowSet... All FCS files have the same following channels: Pulse Width FS Log SS Log FL 1 Log FL 2 Log FL 3 Log FL 4 Log FL 5 Log FL 6 Log TIME Raw Time Sort Classifier done! loading data: ./FlowRepositoryFR-FCM-ZZP6files/113-3d15.fcs No compensation gating ... Error in .cppgating(gs@pointer, mat, guid, gains, nodeInd, recompute, : ellipsoidGate::transforming can't find transformation for FL 4 Log

> sessionInfo()

R version 3.6.0 (2019-04-26) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale: [1] LCCOLLATE=GermanGermany.1252 LCCTYPE=GermanGermany.1252 LCMONETARY=GermanGermany.1252 [4] LCNUMERIC=C LCTIME=German_Germany.1252

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

other attached packages: [1] CytoML1.10.0 flowDiv2.0 gridExtra2.3 ggplot23.1.1
[5] vegan2.5-5 lattice0.20-38 permute0.9-5 flowWorkspace3.32.0
[9] ncdfFlow2.30.1 BH1.69.0-1 RcppArmadillo0.9.700.2.0 flowCore1.50.0

flowworkspace • 79 views
ADD COMMENTlink written 18 days ago by jokup1010
1

It's a little hard to say without seeing the workspace. Would you be able to provide me with the workspace file somehow? Email would be fine: jpwagner@fredhutch.org. It seems strange that it would error out at Log FL 4 (rather than right away at Log FL 1) which makes me think there is something wrong with the workspace file itself.

I can get the FCS files from FlowRepository, so don't worry about those.

ADD REPLYlink written 18 days ago by Jake Wagner130
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