Hello, I'm not sure if this is a known issue, but I have been experiencing unpredictable results with the warpSet function in flowStats (see sessionInfo at end). Essentially, I have a been experimenting with warpSet and have it in a script that runs through the same 5 fcs files as a flowSet each time. About every 2 out of 3 runs I get this error with warpSet: pars <- colnames(Data(wf[["base view"]]))[c(12,13,18,19)] norm <- normalization(normFun = function(x, parameters, ...) + warpSet(x, parameters, ...), + parameters = pars, + normalizationId= "Warping4") add(wf, norm, parent="Lymphs+") Estimating landmarks for channel APC.H7.A ... Registering curves for parameter Pacific.Blue.A ... Registering curves for parameter AmCyan.A ... Error adding item 'action': Error in apply(sapply(regions[!nar], function(r) if (is.null(dim(r))) r else r[n, : dim(X) must have a positive length I'm not clear why it would work sometimes and not work other times. Can anyone point me in the right direction to debug this a bit? Thanks, Aric ============== The full short script up until this section follows: wf <- workFlow(fs, name="2009_03_05 Asinh Workflow") boundaryfilter <- boundaryFilter(filterId = "boundaryfilter", x = c("FSC.A", "SSC.A")) add(wf, boundaryfilter) singletfilter = polygonGate(`FSC.A` = c(10000,13000,20000,40000,60000,80000,100000,160000,200000,263000,2630 00, 200000,160000,100000,80000,60000,40000,20000,14000,8000), `FSC.H` = c(5000,5000,10000,22000,34000,50000,65000,115000,150000,200000,220000, 170000,130000,78000,62000,45000,30000,15000,10000,5000), filterId="Singlet") add(wf, singletfilter, parent="boundaryfilter+") asinhtf <- transformList(colnames(fs)[4:19], asinh, transformationId="asinh") add(wf, asinhtf, parent="Singlet+") lymphfilter <- lymphGate(Data(wf[["asinh"]]), channels=c("FSC.A", "SSC.A"), preselection="APC.H7.A", filterId="Lymphs", eval=FALSE, scale=2) add(wf, lymphfilter$n2gate, parent="asinh") pars <- colnames(Data(wf[["base view"]]))[c(10,11,12,13,18,19)] # problem with 18 norm <- normalization(normFun = function(x, parameters, ...) warpSet(x, parameters, ...), parameters = pars, normalizationId= "Warping") add(wf, norm, parent="Lymphs+") qgate <- quadrantGate(Data(wf[["Warping"]]), stains=c("AmCyan.A", "APC.H7.A"), plot=FALSE, filterId="CD3CD4", positive=T) add(wf, qgate, parent="Warping") ================ sessionInfo() R version 2.11.0 (2010-04-22) amd64-portbld-freebsd8.0 locale: [1] C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] flowStats_1.6.0 cluster_1.12.3 fda_2.2.1 [4] zoo_1.6-3 flowQ_1.8.0 latticeExtra_0.6-11 [7] RColorBrewer_1.0-2 parody_1.6.0 bioDist_1.20.0 [10] KernSmooth_2.23-3 mvoutlier_1.4 outliers_0.13-2 [13] flowViz_1.12.0 lattice_0.18-5 flowCore_1.14.1 [16] rrcov_1.0-00 pcaPP_1.8-1 mvtnorm_0.9-9 [19] robustbase_0.5-0-1 Biobase_2.8.0 fortunes_1.3-7 loaded via a namespace (and not attached): [1] AnnotationDbi_1.10.1 DBI_0.2-5 MASS_7.3-5 [4] RSQLite_0.9-0 annotate_1.26.0 feature_1.2.4 [7] geneplotter_1.26.0 graph_1.26.0 grid_2.11.0 [10] ks_1.6.12 stats4_2.11.0 xtable_1.5-6

Hi, Aric, I've never seen this type error before, but I guess the bugs occur when the warpSet.R is trying to identify the landmarks of the density kernel estimates of one of the stain channel. Is it possible for you to send me the flowSet so that I can reproduce the error and possibly fix the bugs? Thanks, Chao-Jen On 06/02/10 19:46, Aric Gregson wrote: > Hello, > > I'm not sure if this is a known issue, but I have been experiencing > unpredictable results with the warpSet function in flowStats (see > sessionInfo at end). Essentially, I have a been experimenting with warpSet > and have it in a script that runs through the same 5 fcs files as a flowSet > each time. About every 2 out of 3 runs I get this error with warpSet: > > pars <- colnames(Data(wf[["base view"]]))[c(12,13,18,19)] > norm <- normalization(normFun = function(x, parameters, ...) > + warpSet(x, parameters, ...), > + parameters = pars, > + normalizationId= "Warping4") > add(wf, norm, parent="Lymphs+") > Estimating landmarks for channel APC.H7.A ... > Registering curves for parameter Pacific.Blue.A ... > Registering curves for parameter AmCyan.A ... > Error adding item 'action': > Error in apply(sapply(regions[!nar], function(r) if (is.null(dim(r))) r > else r[n, : dim(X) must have a positive length > > I'm not clear why it would work sometimes and not work other times. Can > anyone point me in the right direction to debug this a bit? > > Thanks, Aric > ============== > The full short script up until this section follows: > > wf <- workFlow(fs, name="2009_03_05 Asinh Workflow") > boundaryfilter <- boundaryFilter(filterId = "boundaryfilter", > x = c("FSC.A", "SSC.A")) > add(wf, boundaryfilter) > singletfilter = polygonGate(`FSC.A` = > c(10000,13000,20000,40000,60000,80000,100000,160000,200000,263000,26 3000, > 200000,160000,100000,80000,60000,40000,20000,14000,8000), > `FSC.H` = > c(5000,5000,10000,22000,34000,50000,65000,115000,150000,200000,22000 0,170000,130000,78000,62000,45000,30000,15000,10000,5000), > filterId="Singlet") > add(wf, singletfilter, parent="boundaryfilter+") > asinhtf <- transformList(colnames(fs)[4:19], > asinh, > transformationId="asinh") > add(wf, asinhtf, parent="Singlet+") > lymphfilter <- lymphGate(Data(wf[["asinh"]]), channels=c("FSC.A", "SSC.A"), > preselection="APC.H7.A", filterId="Lymphs", eval=FALSE, scale=2) > add(wf, lymphfilter$n2gate, parent="asinh") > pars <- colnames(Data(wf[["base view"]]))[c(10,11,12,13,18,19)] # problem > with 18 > norm <- normalization(normFun = function(x, parameters, ...) > warpSet(x, parameters, ...), > parameters = pars, > normalizationId= "Warping") > add(wf, norm, parent="Lymphs+") > qgate <- quadrantGate(Data(wf[["Warping"]]), > stains=c("AmCyan.A", "APC.H7.A"), > plot=FALSE, > filterId="CD3CD4", > positive=T) > add(wf, qgate, parent="Warping") > ================ > sessionInfo() > R version 2.11.0 (2010-04-22) > amd64-portbld-freebsd8.0 > > locale: > [1] C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] flowStats_1.6.0 cluster_1.12.3 fda_2.2.1 > [4] zoo_1.6-3 flowQ_1.8.0 latticeExtra_0.6-11 > [7] RColorBrewer_1.0-2 parody_1.6.0 bioDist_1.20.0 > [10] KernSmooth_2.23-3 mvoutlier_1.4 outliers_0.13-2 > [13] flowViz_1.12.0 lattice_0.18-5 flowCore_1.14.1 > [16] rrcov_1.0-00 pcaPP_1.8-1 mvtnorm_0.9-9 > [19] robustbase_0.5-0-1 Biobase_2.8.0 fortunes_1.3-7 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.10.1 DBI_0.2-5 MASS_7.3-5 > [4] RSQLite_0.9-0 annotate_1.26.0 feature_1.2.4 > [7] geneplotter_1.26.0 graph_1.26.0 grid_2.11.0 > [10] ks_1.6.12 stats4_2.11.0 xtable_1.5-6 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org