uploading xml file in flowworkspace
1
1
Entering edit mode
@ekaterina-terskikh-12710
Last seen 6.9 years ago
Switzerland/Zurich/University of Zurich

Hi,

I recently started to work with flowworkspace package in R and have the constant problem.

While opening the xml file, which I exported from FlowJo it gives me errow:

dataDir <- "....."
wsfile <- list.files(dataDir, pattern="wth group.xml",full=TRUE)
ws <- openWorkspace(wsfile)

Error in xpathApply(x, "/Workspace", function(x) xmlGetAttr(x, "version"))[[1]] : 
  subscript out of bounds

I would really appreciate if someone could help me to find out the mistake.

Best,

Ekaterina

flowworkspace xml R flowjo • 2.0k views
ADD COMMENT
0
Entering edit mode
Abby Moore • 0
@abby-moore-22382
Last seen 4.3 years ago
University of Georgia

This is an old post that I came across when I encountered the same error. I'm sharing my solution in case it helps someone else avoid a simple mistake.

In the above issue, it appears that the user is trying to read-in a .xml with the function openWorkspace from the flowWorkspace package, which has now moved to the CytoML package. Within this package, there are a couple options for opening workspace data, namely open_flowjo_xml and open_diva_xml.

In my case, I was trying to read-in public data with the open_flowjo_xml function when I received the above error:

flowDataPath <- "~/my_dir"
wsfile <- list.files(flowDataPath, pattern="Fig_1_expt.xml",full = TRUE)
path <-  open_flowjo_xml(wsfile)

The error was produced because my files were actually produced with Diva, not FlowJo, so the following worked:

flowDataPath <- "~/my_dir"
wsfile <- list.files(flowDataPath, pattern="Fig_1_expt.xml",full = TRUE)
path <- open_diva_xml(wsfile)
ADD COMMENT

Login before adding your answer.

Traffic: 756 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6