[BioC] cellHTS2 writeReport error

[Becky Saunders]

Sorry, I didn't think you would need it.

Here it is.

Many thanks. 

-----Original Message-----
From: rclement [mailto:rclement at ebi.ac.uk] 
Sent: 17 July 2008 09:47
To: Becky Saunders
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] cellHTS2 writeReport error

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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> London Research Institute
> Cancer Research UK
>
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>
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>
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