Question

openCyto trouble importing xml file

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Rivka • 0

@rivka-11959

Last seen 7.4 years ago

Munich

Hello,

I am very new to openCyto and trying to import a xml file (being a workspace from FlowJo.) I keep getting an error saying

"Error in xpathApply(x, "/Workspace", function(x) xmlGetAttr(x, "version"))[[1]] : Indexing beyond border

# Open workspace
wsfile<-"flowjo_ws.xml"
ws<-openWorkspace(wsfile)

Fehler in xpathApply(x, "/Workspace", function(x) xmlGetAttr(x, "version"))[[1]] :
Indizierung außerhalb der Grenzen

Thanks, Rivka

opencyto bioconductor R • 1.8k views

ADD COMMENT • link 8.0 years ago Rivka • 0

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Rivka • 0

@rivka-11959

Last seen 7.4 years ago

Munich

Hey,

it was a problem of the xml-file itself. I fixed it and now it's working.

ADD COMMENT • link 8.0 years ago Rivka • 0

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Hey,

Could you please explain what you changed in your xml file? I have the same problem to import workspace from flowjo.

Thanks a lot in advance!

Ekaterina

ADD REPLY • link 7.7 years ago Ekaterina Terskikh ▴ 10

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Hello,

sorry I did not see your comment earlier due to our new baby:-)

What I changed: I did not use the actual xml file but just the workspace,that you can download from flowjo, and has the suffix .wsp and that worked for me. See picture more more information: https://goo.gl/photos/KcK9CDTAvfkTqhddA

Rivka

ADD REPLY • link 7.5 years ago Rivka • 0

score 1 · Accepted Answer · 2016-12-02

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Jiang, Mike ★ 1.3k

@jiang-mike-4886

Last seen 3.1 years ago

(Private Address)

Looks like the version information is missing in your xml file. Could you send it to wjiang2@fhcrc.org and I can take a look at it?

ADD COMMENT • link 8.0 years ago Jiang, Mike ★ 1.3k