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

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