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Hill, Andrew
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@hill-andrew-4675
Last seen 10.2 years ago
Folks,
Could anyone provide any advice to resolve the error "the leading
minor
of order 6 is not positive definite" in the flowStats warpSet()
function? Are negative SSC values problematic? Error transcript,
traceback and sessionInfo() are below.
Any pointers much appreciated,
Andrew Hill.
> ret.f1.aligned <- warpSet(ret.f1[2:4], c("SSC","CD45"))
Estimating landmarks for channel CD45 ...
Registering curves for parameter SSC ...
Error in chol.default(Asym) :
the leading minor of order 6 is not positive definite
> traceback()
13: .Call("La_chol", as.matrix(x), PACKAGE = "base")
12: chol.default(Asym)
11: chol(Asym)
10: symsolve(hessmat, Flist$grad)
9: linesearch.smooth.morph(Flist, hessmat, dbglev)
8: smooth.morph(xval, yval, WfdPar)
7: landmarkreg(fdobj, landmarks, WfdPar = WfdPar, monwrd = monwrd,
...)
6: eval(expr, envir, enclos)
5: eval(expr, pf)
4: withVisible(eval(expr, pf))
3: evalVis(expr)
2: capture.output(regDens <- landmarkreg(fdobj, landmarks, WfdPar =
WfdPar,
monwrd = monwrd, ...))
1: warpSet(ret.f1[2:4], c("SSC", "CD45"))
> ret.f1
A flowSet with 20 experiments.
An object of class "AnnotatedDataFrame"
rowNames: <..snip..> (20 total)
varLabels: <...snip..>... Total.Damage.Score (115 total)
varMetadata: labelDescription
column names:
SSC CD45
> do.call("cbind",summary(ret.f1[,"SSC"]))
SSC SSC SSC SSC SSC SSC SSC SSC
SSC
Min. 2261 1934 268.8 -8791000 4763 4204 -8683000 2048
1992
1st Qu. 57360 27130 14930.0 13260 51160 14530 22090 65940
94290
Median 97900 91620 27190.0 26260 131700 34020 117000 112400
124000
Mean 89660 82570 60440.0 -10950 113800 63580 86300 103000
116800
3rd Qu. 120700 121600 107900.0 132800 160900 114300 151000 136700
149600
Max. 262100 262100 262100.0 262100 262100 262100 262100 262100
262100
SSC SSC SSC SSC SSC SSC SSC SSC
SSC
Min. -60080 5147 -450.5 3594 -55360 1834 3173 3043
-8493000
1st Qu. 52640 32330 20260.0 18420 19210 43810 15090 19980
15820
Median 96830 110100 76910.0 109400 88820 80520 35470 39070
55720
Mean 93650 96740 68640.0 90390 77760 79980 62560 65690
39280
3rd Qu. 118800 135300 98780.0 142700 111900 107500 110800 107100
136400
Max. 262100 262100 262100.0 262100 262100 262100 262100 262100
262100
SSC SSC
Min. 4443 716.9
1st Qu. 21060 17850.0
Median 47510 67560.0
Mean 77130 84110.0
3rd Qu. 131400 143300.0
Max. 262100 262100.0
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] splines stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] bsub_1.0.0 flowStats_1.10.0 cluster_1.13.3
[4] mvoutlier_1.8 robCompositions_1.5.0 car_2.0-10
[7] survival_2.36-5 nnet_7.3-1 compositions_1.10-1
[10] energy_1.3-0 MASS_7.3-12 boot_1.2-43
[13] tensorA_0.36 rgl_0.92.798 fda_2.2.6
[16] zoo_1.6-5 flowViz_1.16.0 lattice_0.19-26
[19] flowCore_1.18.0 rrcov_1.3-00 pcaPP_1.8-3
[22] mvtnorm_0.9-999 robustbase_0.7-3 Biobase_2.12.1
loaded via a namespace (and not attached):
[1] KernSmooth_2.23-4 RColorBrewer_1.0-2 feature_1.2.7
[4] graph_1.30.0 grid_2.13.0 ks_1.8.1
[7] latticeExtra_0.6-16 stats4_2.13.0 tcltk_2.13.0
[10] tools_2.13.0