reading an ".xml" file as FlowJo Workspace file
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anara92 • 0
Last seen 7.9 years ago

Hi, everyone. I am new to R and Bioconductor, but want to say thank you to the creators for sharing all the materials for free. This is an amazing source for all of us.

I'm working with the openCyto package to compare manually (flowJo) analyzed clinical data with openCyto analysis.
I am experiencing an issue while opening a FlowJo (version 10.0.8) Workspace file for using it as a gating template. The problems are:
1) FlowJo cannot save the workspace as .xml format file, which seems to be the only format that openWorkspace() function takes while opening the gating template;
My flowJo version only saves the workspace as .wspt or .xls files, and I even converted my gating template to .xml file, but openWorkspace() function still does not open the file in any format. WHen opening as .xml file, it gives the following error:
Error in xpathApply(x,"/Workspace",function(x) xmlGetAttrx(x,"version")) [[1]]: subscript out of bounds.

2) I also tried to create/use my own template as .csv file. However, I don't know how to do the compensation (specify the compensation values) that are usually automatically given in the fcs metadata..Since almost every single .fcs file (1 patient) in my Flowset has different compensation matrix (because we had the results of the patients on different weeks), I cannot write single spillover values in the pre-processing column of a gating template that i'm creating.

So, my questions would be: how can I use .xls or .wspt Workspace gating template from FlowJo (10.0.8) to open it & use it as my gating template in openCyto? (possibly with openWorkspace function or nay other way)? And, how do I compensate my flowSet, if every single sample/.fcs file of my flowSet has to have different compensation matrix?
I'm sure there must be people who have encountered this problem (having to receive results at different times points and apply several compensation matrices to one flwoSet).
I would greatly appreciate any advice on these questions,or,any advice in general of ways to analyze 60 .fcs file-flowSet (acquired at different time points) with 15 channels.

opencyto gating opencyto flowcore flowworkspace • 2.2k views
Entering edit mode
Jiang, Mike ★ 1.3k
Last seen 2.6 years ago
(Private Address)

1) flowJo template is currently not supported yet. Please vote for the feature request here if you do think it is important

2) You normally should separate the compensation and transformation from the csv template since the csv is dedicated for gating purpose. Given the compensation is sample-specific, the code probably goes like this

fs.comp <- fsApply(fs.raw, function(fr){
                      #extract compensation matrix from FCS keyword
                      comp <- spillover(fr)[["SPILL"]] #keyward name could be "spillover"
                      #compensate and return the data
                      compensate(fr, comp) 

Once you are done with these data preprocessing, I'd highly recommend you to convert 'flowSet' to hdf2-based 'ncdfFlowSet' before running gating template because the latter is more memory efficient and could be even faster. e.g

ncfs <- ncdfFlowSet(fs.comp)
gs <- GatingSet(ncfs)






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