[BioC] flowCore / flowViz: densityplot of FCS file without time channel

Florian Hahne fhahne at fhcrc.org
Tue Apr 7 18:00:11 CEST 2009


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]]
>
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