Trouble parsing a workspace in flowWorkspace
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wir.traumen ▴ 10
@wirtraumen-10008
Last seen 5.6 years ago

Sample groups aren't recognized when trying to parse workspaces. I've tried loading wsp files from flowJo version X, as well as xml's saved from flowJo versions 8, 9, and X. This error occurs with any fcs generated from FACS, but does NOT occur for any samples acquired on the CyTOF.

> ws
FlowJo Workspace Version  2.0 
File location:  /Users/kmc/Documents/fcsCopiesForOpenCytoTrial 
File name:  HBRN_Tcell.xml 
Workspace is open. 

Groups in Workspace
         Name Num.Samples
1 All Samples           1
> gs <- parseWorkspace(ws, isNcdf = TRUE)
Choose which group of samples to import:

 

Selection: 1
Enter an item from the menu, or 0 to exit

 

When I specify the sample group ahead of time I get this:

gs <- parseWorkspace(ws, name = 1, isNcdf = TRUE)

Error in .preprocessor(obj, ...) : Invalid sample group index.

flowworkspace opencyto • 1.0k views
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lovetatting ▴ 10
@lovetatting-9329
Last seen 5.2 years ago
Sweden

HI,

I understand that you don't have any sample groups in your FlowJo-file other than "All Samples" and that it works fine when you do it interactively, but not when you try to do it in call to parseWorkspace. 

The offending code is at 216 in flowWorkspace-Methods.R

So, what's happening is that when you supply a number interactively, there is no error checking and it goes straight to picking your group from the groups. When you supply name as a numeric, it will check that your number is lesser than the actual number of groups. However, as it is doing it with the less than operator "<" and not the less than or equal operator "<=", there is no way for you to supply name as a numeric if you don't have sample groups other than All Samples. This is because nothing can be less than 1 and not 0. (If you write name=-1 it will probably work as well). Best is to be explicit, and if you instead write name="All Samples", it should work fine. 

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