Error: Unable to match stains with controls based on intensity: a single stain matches to several multiple controls. - Spillover-flowcore
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Entering edit mode
@davidefranchina-10185
Last seen 5.8 years ago
Luxembourg

Dear all,

 

 

I am writing to enquire about the spillover function of FlowCore. I am stucked because of an error in matching intensity between the controls.

I am trying to set up my compensation matrix from my flowset(it contains the unstained ctrl + single stained compensation ctrls, ordered 1 to 8 as 1unstained-2FITC, 3PE, 4PE-tr, 5PerCP, 6APC-7, APCCy7, 8PB).

here is my piece o code:

fs[, delcolnames]
A flowSet with 8 experiments.

 column names:
 FSC-A FITC-A PE-A PE-TexasRed-A PerCP-A APC-A APC-Cy7-A Pacific Blue-A

com.mat=spillover(fs[, delcolnames], unstained = "1.Compensation Controls_Unstained Control.fcs", fsc = "FSC-A", ssc = "SSC-A", method = "median", stain_match = c("intensity", "ordered", "regexpr"), useNormFilt=FALSE, pregate = FALSE, plot = FALSE)

Error: Unable to match stains with controls based on intensity: a single stain matches to several multiple controls. 

> traceback()
4: stop("Unable to match stains with controls based on intensity: ", 
       "a single stain matches to several multiple controls. ", 
       call. = FALSE)
3: .local(x, ...)
2: spillover(fs[, delcolnames], unstained = "1.Compensation Controls_Unstained Control.fcs", 
       fsc = "FSC-A", ssc = "SSC-A", method = "median", stain_match = c("intensity", 
           "ordered", "regexpr"), useNormFilt = FALSE, pregate = FALSE, 
       plot = FALSE)
1: spillover(fs[, delcolnames], unstained = "1.Compensation Controls_Unstained Control.fcs", 
       fsc = "FSC-A", ssc = "SSC-A", method = "median", stain_match = c("intensity", 
           "ordered", "regexpr"), useNormFilt = FALSE, pregate = FALSE, 
       plot = FALSE)

 

 

could please anyone help me? any comments would be much appreciated

thank you in advance!

 

 

spillover compensation flowcore • 1.0k views
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Entering edit mode
Jiang, Mike ★ 1.3k
@jiang-mike-4886
Last seen 11 months ago
(Private Address)

Maybe this will help you. A: spillover::flowCore problem: Error in match(unstained, sampleNames(x))

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Entering edit mode
@davidefranchina-10185
Last seen 5.8 years ago
Luxembourg

Hi Mike,

Thank you very much, I just read...

Anyway, I couldn,t solve the problem.

I have tried several "method" and "stain_match" or changing the name of the unstained negative control.

It keeps returning the error

Error: Multiple stains match to a common compensation-control filename 
or 

Error: Unable to match stains with controls based on intensity: a single stain matches to several multiple controls. 
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