Question: flowDensity error only with upper=TRUE and alpha=0.001 arguments used together
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gravatar for rschmidt2
4.5 years ago by
rschmidt20
United States
rschmidt20 wrote:

Hi,

I have encountered an error with only certain flowFrames when using flowDensity with both the arguments upper=TRUE and alpha=0.001.  The error is not generated when I remove either of these arguments.  However, I do not get the exact gating that I want unless both arguments are present.  Strangely, in the past, I was able to run flowDensity using both of these arguments on all of the flowFrames in my flowSet without errors, and I have the plots saved.  I could really use some help in figuring out how to get past these errors.  See below for my code.

Thanks for your help!

Ryan

> class(fs.comp.lgcl)
[1] "flowSet"
attr(,"package")
[1] "flowCore"
> summary(fs.comp.lgcl[[1]])
        FSC-A  SSC-A  FITC-A    PE-A PerCP-A   APC-A    Time
Min.    3.225 -1.056 -0.2647 -0.3594 -1.6200 -0.5124     0.2
1st Qu. 3.996  3.665  1.3130  1.1400  0.7418  1.6420  6971.0
Median  4.294  4.394  1.5260  1.4450  1.2070  1.8750 13910.0
Mean    4.192  4.126  1.5230  1.4220  1.1200  2.0080 13890.0
3rd Qu. 4.427  4.500  1.6980  1.6550  1.4880  2.1280 20800.0
Max.    4.500  4.500  4.5000  4.4990  4.4930  4.5000 27740.0
> summary(fs.comp.lgcl[[12]])
        FSC-A  SSC-A  FITC-A    PE-A PerCP-A   APC-A  Time
Min.    2.167 -1.557 -0.6502 -0.6558  -1.166 -1.8670     0
1st Qu. 3.939  3.755  1.1300  0.9708   0.825  0.9897  3097
Median  4.283  4.322  1.4000  1.3220   1.215  1.4370  6081
Mean    4.120  4.101  1.3770  1.3200   1.167  1.3780  6047
3rd Qu. 4.363  4.446  1.6290  1.6150   1.495  1.7270  9031
Max.    4.500  4.500  4.4960  4.4990   4.472  4.4970 11890
> #NOTE: the error is generated with flowFrame 1, but not with flowFrame 12
> gate <- flowDensity(obj=fs.comp.lgcl[[12]], channels=c("PE-A","FSC-A"),position=c(TRUE,TRUE),upper=TRUE, alpha=0.001,ellip.gate=TRUE)
> gate <- flowDensity(obj=fs.comp.lgcl[[1]], channels=c("PE-A","FSC-A"),position=c(TRUE,TRUE),upper=TRUE, alpha=0.001,ellip.gate=TRUE)
Error in cov.wt(cbind(x, y), wt = weights) :
  weights must be non-negative and not all zero
> #NOTE: now if I take away either the upper=TRUE or the alpha=0.001 argument, I do not get an error
> gate <- flowDensity(obj=fs.comp.lgcl[[1]], channels=c("PE-A","FSC-A"),position=c(TRUE,TRUE),upper=TRUE,ellip.gate=TRUE)
> gate <- flowDensity(obj=fs.comp.lgcl[[1]], channels=c("PE-A","FSC-A"),position=c(TRUE,TRUE),alpha=0.001,ellip.gate=TRUE)

flowdensity • 617 views
ADD COMMENTlink written 4.5 years ago by rschmidt20
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