getIndices identifies non existing cells in a gate
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helena_t • 0
@helena_t-10046
Last seen 4.9 years ago
Hi,

I have issues with the getIndices() function from the flowWorkspace package. It identifies much more cells as "TRUE" for a gate than it should. Here's my code:

wspath<-"~/Desktop/workspc.wsp"
ws<-openWorkspace(wspath)
G <- parseWorkspace(ws,name=1)
nodelist<-getNodes(G[[1]])

num_f5<-grep(pattern = paste("/F5\$"),nodelist)
f5<-nodelist[num_f5]
summary(getIndices(G[[1]],f5))​

I have no clue why getIndices() doesn't identify the right cells in the gate I'm interested in, it works perfectly for the gates on top of the gate "F5" in my gating strategy.

Helena

flowworkspace getIndices • 762 views
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 3 months ago

First of all, If you just want to get the cells within that gate, you can simply do

getData(G[[1]], f5)

To check if the parsing went well, do

getPopStats(G[[1]])

which will give you the comparison between the flowJo counts and flowWorkspace counts as the validity checks. If they are significantly different (at some gates), then there is parsing problem and you will need to provide more info about the flowjo workspace.

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helena_t • 0
@helena_t-10046
Last seen 4.9 years ago

The problem is exactly the same with getData(): I have much more F5 cells than expected.

I ran getPopStats and the flowCore counts are clearly very different from the flowJo counts. The flowJo gate that flowWorkspace doesn't manage to read properly is an ellipse. I tried replacing it by a polygon gate. The flowCore counts are closer to the flowJo counts now, but there is still a significant difference.

Is there any argument I could give to getIndices() which would force the function to take the cells that are really in the flowJo gate, and not the cells that flowCore imagines are in the gate?

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If the gates are not parsed correctly, we then need to fix the parsing first. Can you make sure you have the latest version of flowWorkspace package (i.e. 3.20.4)? If so,  Can you share your example workspace and FCS for me to trouble shoot? (You can send them to wjiang2@fhcrc.org)

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helena_t • 0
@helena_t-10046
Last seen 4.9 years ago

I downloaded the latest version of flowWorkspace (3.20.4), but unfortunately it didn't help. I just sent the FCS file and workspace that FlowWorkspace doesn't parse properly to the email address you indicated.

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Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 3 months ago

The fix is in flowWorkspace 3.20.5. Bioconductor should build within 1 day or two.

see the correct F5 gate here https://github.com/RGLab/flowWorkspace/issues/142#issuecomment-280752179