Question: Problem parsing data with parseWorkspace
0
gravatar for jokup101
10 weeks 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 • 137 views
ADD COMMENTlink written 10 weeks 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 10 weeks ago by Jake Wagner130

Your workspace was produced by FlowJo version 7.6.5, which handled Logicle transformations significantly differently. I took your workspace and loaded it in to FlowJo version 10.6.1, which itself raised a dialog box to emphasize the changes since the old version:

"This workspace has one or more parameters using the Logicle transform. Because the implementation of this transform has been updated, any gates on these populations will need to be adjusted."

Sure enough, the gates were off for Logicle-transformed channels, but I still re-exported it to see if CytoML could handle the re-exported XML. CytoML::parseWorkspace can indeed parse the re-exported XML, but it has the same issue as FlowJo 10.6.1 of misplaced gates due to the change in the Logicle transform, so those will need to fixed.

I am not sure when we will have a chance to devote time to this backwards compatibility, but I will post here when progress is made on that front. For now I will e-mail you the re-exported workspace XML that is CytoML-compatible.

ADD REPLYlink written 6 weeks ago by Jake Wagner130

Thanks a lot for the support! The re-exported workspace loads with no issues. Luckily we just switched to the newest version of FlowJo so this shouldn't be a problem for us in the future.

ADD REPLYlink written 5 weeks ago by jokup1010
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