[BioC] cellHTS2 writeReport error

[rclement]

Hi Becky,

could you please also send the file  "description.txt" ?

Thanks
Remy


Becky Saunders wrote:
> Hi there,
>  
> Could someone help me with the following error when I try to execute the
> writeReport command using cellHTS2 version 2.4.0, R version 2.7.0.
>  
> out <- writeReport(cellHTSlist=list(raw=x), outdir=file.path(outHTMLDir,
> "raw"), force=TRUE)
>
> Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx =
> pdim(x)[["ncol"]],  :  'fill' must have length >=2 since it is used to
> compute the color ramp that represent the values in z.
>
> I think the problem originates because I have not set a positive control
> in my plateConf file, as when I run the exact same input files with a
> positive control set it works fine. Is it possible to run the analysis
> without a positive control set?
>  
> Also is it possible to set an argument to not include the
> configurationAsScreenPlot figure in the report, as you can do for
> plotPlateArgs and imageScreenArgs when you call writeReport?
>  
> Many Thanks,
>  
> Becky 
>
>
> ===========R Console =================
>
>   
>> x <- readPlateList("plateList.txt", name="Automated Preliminary
>>     
> Analysis", path=dataPath)
> Automated Preliminary Analysis: found data in 8 x 12 (96 well) format.
>
> Reading 1: plate_1.txt
> Read 1 plates.             
>  
>   
>> descripFile = file.path(dataPath, "description.txt")
>> confFile= file.path(dataPath, "plateConf.txt")
>> x <- configure(x, confFile=confFile, descripFile=descripFile)
>> out <- writeReport(cellHTSlist=list(raw=x), outdir=file.path(dataPath,
>>     
> "raw"), force=TRUE)
> Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx =
> pdim(x)[["ncol"]],  : 
>   'fill' must have length >=2 since it is used to compute the color ramp
> that represent the values in z.
>
>
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>
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