dear flowCore/flowViz developers, i got some FCS files to analyse and always wondered about a strange error message once i tried to create a densityplot: Error in apply(xx, 2, function(y) all(sign(diff(y)) >= 0)) : dim(X) must have a positive length until i finally found out that this error is thrown by the flowCore:::findTimeChannel function. actually i do not have a channel in the FCS files recording the time and the code in the function cont <- apply( xx, 2 , function(y)all(sign(diff(y)) >= 0) ) throws the error, since xx is, in this case, a flowSet object and not a matrix or data.frame I'm just wondering if the function flowCore:::findTimeChannel really has to be called in the densityplot function for flowSets, since this function will always result in an error if there is no column named Time. I finally realized that by calling densityplot and specifying the channels i can circumvent the problem > densityplot( ~., C2C8, channels="FSC-H" ) # works > densityplot( ~`FSC-H`, C2C8 ) Error in apply(xx, 2, function(y) all(sign(diff(y)) >= 0)) : dim(X) must have a positive length however it would be nice if als the first call would work... bests, jo my sessionInfo: > sessionInfo() R version 2.8.0 (2008-10-20) i386-apple-darwin9.5.0 locale: en_US.ISO8859-1/en_US.ISO8859-1/C/C/en_US.ISO8859-1/en_US.ISO8859-1 attached base packages: [1] tools tcltk stats graphics grDevices utils datasets [8] methods base other attached packages: [1] xtable_1.5-4 flowViz_1.6.2 latticeExtra_0.5-4 lattice_0.17-15 [5] RColorBrewer_1.0-2 flowCore_1.8.3 Biobase_2.2.1 feature_1.2.2 [9] ks_1.6.2 rpanel_1.0-5 KernSmooth_2.22-22 rrcov_0.5-01 [13] pcaPP_1.6 mvtnorm_0.9-5 robustbase_0.4-5 loaded via a namespace (and not attached): [1] AnnotationDbi_1.4.1 DBI_0.2-4 MASS_7.2-44 [4] RSQLite_0.7-1 cluster_1.11.11 geneplotter_1.20.0 [7] graph_1.20.0 grid_2.8.0 stats4_2.8.0 -- Johannes Rainer, PhD Bioinformatics Group, Division Molecular Pathophysiology, Biocenter, Medical University Innsbruck, Fritz-Pregl-Str 3/IV, 6020 Innsbruck, Austria and Tyrolean Cancer Research Institute Innrain 66, 6020 Innsbruck, Austria Tel.: +43 512 570485 33 Email: johannes.rainer@i-med.ac.at johannes.rainer@tcri.at URL: http://bioinfo.i-med.ac.at [[alternative HTML version deleted]]

Hi Johannes, thanks for this info. I recently fixed a similar issue regarding the detection of the time channel, but this seems to be something else. The function can deal with flowSets and flowFrames, so that shouldn't be the problem. Could you send me one of your FCS files so that I can take a closer look, please? Thanks, Florian On 07.04.2009, at 03:44, Johannes Rainer wrote: > dear flowCore/flowViz developers, > > i got some FCS files to analyse and always wondered about a strange > error > message once i tried to create a densityplot: > Error in apply(xx, 2, function(y) all(sign(diff(y)) >= 0)) : > dim(X) must have a positive length > > until i finally found out that this error is thrown by the > flowCore:::findTimeChannel function. actually i do not have a > channel in the > FCS files recording the time > and the code in the function > > cont <- apply( xx, 2 , function(y)all(sign(diff(y)) >= 0) ) > > throws the error, since xx is, in this case, a flowSet object and > not a > matrix or data.frame > > I'm just wondering if the function flowCore:::findTimeChannel really > has to > be called in the densityplot function for flowSets, since this > function will > always result in an error if there is no column named Time. > > I finally realized that by calling densityplot and specifying the > channels i > can circumvent the problem > > >> densityplot( ~., C2C8, channels="FSC-H" ) # works > >> densityplot( ~`FSC-H`, C2C8 ) > Error in apply(xx, 2, function(y) all(sign(diff(y)) >= 0)) : > dim(X) must have a positive length > > however it would be nice if als the first call would work... > > bests, jo > > > my sessionInfo: > >> sessionInfo() > R version 2.8.0 (2008-10-20) > i386-apple-darwin9.5.0 > > locale: > en_US.ISO8859-1/en_US.ISO8859-1/C/C/en_US.ISO8859-1/en_US.ISO8859-1 > > attached base packages: > [1] tools tcltk stats graphics grDevices utils > datasets > [8] methods base > > other attached packages: > [1] xtable_1.5-4 flowViz_1.6.2 latticeExtra_0.5-4 > lattice_0.17-15 > [5] RColorBrewer_1.0-2 flowCore_1.8.3 Biobase_2.2.1 > feature_1.2.2 > [9] ks_1.6.2 rpanel_1.0-5 KernSmooth_2.22-22 > rrcov_0.5-01 > [13] pcaPP_1.6 mvtnorm_0.9-5 robustbase_0.4-5 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.4.1 DBI_0.2-4 MASS_7.2-44 > [4] RSQLite_0.7-1 cluster_1.11.11 geneplotter_1.20.0 > [7] graph_1.20.0 grid_2.8.0 stats4_2.8.0 > > > > -- > Johannes Rainer, PhD > Bioinformatics Group, > Division Molecular Pathophysiology, > Biocenter, Medical University Innsbruck, > Fritz-Pregl-Str 3/IV, 6020 Innsbruck, Austria > and > Tyrolean Cancer Research Institute > Innrain 66, 6020 Innsbruck, Austria > > Tel.: +43 512 570485 33 > Email: johannes.rainer at i-med.ac.at > johannes.rainer at tcri.at > URL: http://bioinfo.i-med.ac.at > > [[alternative HTML version deleted]] > > _______________________________________________ > 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