flowQ package: qaProcess.marginevents() function doesn't work
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@ewelina-bakala-4110
Last seen 7.2 years ago
hallo everybody, I have a problem with qaProcess.marginevents() function from flowQ package I'm following the example > library(flowQ) > data(GvHD) > dest<- tempdir() > qp<- qaProcess.marginevents(GvHD, channels=c("FSC-H", "SSC-H"), outdir=dest) that I got trying > ?qaProcess.marginevents but the command > qp<- qaProcess.marginevents(GvHD, channels=c("FSC-H", "SSC-H"), outdir=dest) follows to the error message: computing margin events...Error: no se pudo encontrar la funci?n "boundaryFilter" Error en filter(set, boundaryFilter(x, side = side)) : error in evaluating the argument 'filter' in selecting a method for function 'filter' and I have no idea how to deal with this error.I will be very thankful if you could help me to solve this problem. Best wishes, Ewelina Bakala > sessionInfo() R version 2.10.0 (2009-10-26) i686-pc-linux-gnu locale: [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=es_ES.UTF-8 [7] LC_PAPER=es_ES.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tools tcltk stats graphics grDevices utils datasets [8] methods base other attached packages: [1] flowQ_1.6.0 latticeExtra_0.6-4 RColorBrewer_1.0-2 parody_1.4.0 [5] bioDist_1.18.0 mvoutlier_1.4 flowViz_1.10.0 flowCore_1.8.3 [9] Biobase_2.6.0 feature_1.2.4 ks_1.6.8 rpanel_1.0-5 [13] KernSmooth_2.23-3 rrcov_1.0-00 pcaPP_1.7 mvtnorm_0.9-8 [17] robustbase_0.4-5 lattice_0.17-26 outliers_0.13-2 loaded via a namespace (and not attached): [1] annotate_1.24.0 AnnotationDbi_1.8.0 DBI_0.2-4 [4] geneplotter_1.24.0 graph_1.24.0 grid_2.10.0 [7] MASS_7.3-3 RSQLite_0.7-3 stats4_2.10.0 [10] xtable_1.5-5 >
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@nishant-gopalakrishnan-3253
Last seen 7.2 years ago
Hi Ewelina, You are using the flowQ package (v 1.6.0) from the 2.5 Bioconductor release. However the flowCore package you are using seems to be an older version from the 2.3 release ( v 1.8.3). Perhaps updating your package dependencies might fix the issue. I would recommend updating all your packages to the 2.6 release of Bioconductor. Nishant On 06/02/2010 07:33 AM, Ewelina Bakala wrote: > hallo everybody, > I have a problem with qaProcess.marginevents() function from flowQ > package > I'm following the example > >> library(flowQ) >> data(GvHD) >> dest<- tempdir() >> qp<- qaProcess.marginevents(GvHD, channels=c("FSC-H", "SSC-H"), > outdir=dest) > > that I got trying >> ?qaProcess.marginevents > > but the command >> qp<- qaProcess.marginevents(GvHD, channels=c("FSC-H", "SSC-H"), > outdir=dest) > > follows to the error message: > computing margin events...Error: no se pudo encontrar la funci?n > "boundaryFilter" > Error en filter(set, boundaryFilter(x, side = side)) : > error in evaluating the argument 'filter' in selecting a method for > function 'filter' > > and I have no idea how to deal with this error.I will be very thankful > if you could help me to solve this problem. > > Best wishes, > Ewelina Bakala > > > > >> sessionInfo() > R version 2.10.0 (2009-10-26) > i686-pc-linux-gnu > > locale: > [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C > [3] LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=es_ES.UTF-8 > [7] LC_PAPER=es_ES.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] tools tcltk stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] flowQ_1.6.0 latticeExtra_0.6-4 RColorBrewer_1.0-2 > parody_1.4.0 > [5] bioDist_1.18.0 mvoutlier_1.4 flowViz_1.10.0 > flowCore_1.8.3 > [9] Biobase_2.6.0 feature_1.2.4 ks_1.6.8 > rpanel_1.0-5 > [13] KernSmooth_2.23-3 rrcov_1.0-00 pcaPP_1.7 > mvtnorm_0.9-8 > [17] robustbase_0.4-5 lattice_0.17-26 outliers_0.13-2 > > loaded via a namespace (and not attached): > [1] annotate_1.24.0 AnnotationDbi_1.8.0 DBI_0.2-4 > [4] geneplotter_1.24.0 graph_1.24.0 grid_2.10.0 > [7] MASS_7.3-3 RSQLite_0.7-3 stats4_2.10.0 > [10] xtable_1.5-5 >> > > _______________________________________________ > 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
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