Question: flowStats Plot quadrantGate Filter Result Smooth=FALSE
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gravatar for Chao-Jen Wong
9.0 years ago by
Chao-Jen Wong580
USA/Seattle/Fred Hutchinson Cancer Research Center
Chao-Jen Wong580 wrote:
Hi, Aric We are able to reproduce the error using GvHD dataset. When setting smooth=FALSE and using quadrantGate or quadGate as the filter, the xyplot function would not work. There is certainly a bug in the display functions, and it is in our to-do list to fix it. I will let you know as soon as we fix it. Thanks, Chao-Jen On 07/29/10 18:47, Aric Gregson wrote: > Hello, > > I don't believe that I have seen an explanation and I suspect that I am > not calling the filter appropriately. Using flowStats in a workFlow > with a quadrantGate making a filter I can easily plot the results with > the xyplot if smooth=TRUE (the default). However, when the populations > get small smooth=T is inadequate to visualize the results. Setting > smooth=F results in: > > error in evaluating the argument 'subset' in selecting a method for > 'Subset' > > quad <- quadrantGate(Data(wf[["CD4+CD3+"]]), > stains=c("Pacific.Blue.A","Alexa.Fluor.700.A"), > plot=TRUE, > filterId="quad", > borderQuant=0.3, > alpha=c(1,1), > sd=c(0.6,0.6), > refLine.1=5, > refLine.2=5) > add(wf, quad, parent="CD4+CD3+") > > -> This works fine: > xyplot(`Alexa.Fluor.700.A` ~ `Pacific.Blue.A` | Filename, > Data(wf[['CD4+CD3+']]), > filter=quad) > > -> This fails with the above error message: > xyplot(`Alexa.Fluor.700.A` ~ `Pacific.Blue.A` | Filename, > Data(wf[['CD4+CD3+']]), > smooth=F, > filter=quad) -> I have tried to access gate, boundX/Y but not able > > This is consistent and can be replicated with the GvHD set using a > similar filter setup. > > Thanks in advance. > Aric > > sessionInfo() > R version 2.11.0 (2010-04-22) > amd64-portbld-freebsd8.1 > > locale: > [1] C > > attached base packages: > [1] grid tools splines stats graphics grDevices > utils [8] datasets methods base > > other attached packages: > [1] Rgraphviz_1.26.0 graph_1.26.0 flowQ_1.9.0 > [4] latticeExtra_0.6-11 RColorBrewer_1.0-2 parody_1.6.0 > [7] bioDist_1.20.0 KernSmooth_2.23-3 outliers_0.13-2 > [10] flowStats_1.7.5 cluster_1.12.3 mvoutlier_1.4 > [13] fda_2.2.2 zoo_1.6-4 flowViz_1.13.1 > [16] lattice_0.18-5 flowCore_1.15.2 rrcov_1.0-01 > [19] pcaPP_1.8-2 mvtnorm_0.9-92 robustbase_0.5-0-1 > [22] Biobase_2.8.0 fortunes_1.3-7 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.10.2 DBI_0.2-5 MASS_7.3-5 > [4] RSQLite_0.9-2 annotate_1.26.1 feature_1.2.4 > [7] geneplotter_1.26.0 ks_1.6.13 stats4_2.11.0 > [10] 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
cancer flowstats • 490 views
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