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

Hi Andrew, I am not familiar with the flowStat package, but Cholesky factorization is used to solve system(s) of linear equations where the matrix is symmetric and POSITIVE DEFINITE. All leading minors of positive definite matrix are positive. So your error message means that your matrix is not positive definite. It may be either indefinite (i.e. have both positive and negative eigenvalues) or your matrix may be near singular, i.e. it's smallest eigenvalue is very close to 0 (and so computationally it is 0). Regards, Moshe. > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Moshe Olshansky Division of Bioinformatics The Walter & Eliza Hall Institute of Medical Research 1G Royal Parade, Parkville, Vic 3052 e-mail: olshansky at wehi.edu.au tel: (03) 9345 2697 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}