[BioC] "leading minor...is not positive definite" in flowStats warpSet() function

[Hill, Andrew]

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