[BioC] cellHTS2: help with ConfFile (convertWellCoordinates) function

[Florian Hahne]

Hi Wolfgang,

Wolfgang Huber schrieb:
> Dear Dara,
>
> the attachment didn't get through the mailing list, can you send it to 
> me privately (ideally, send a short example script that allows me to 
> reproduce your error, perhaps with some reduced or toy version of your 
> data) and I'll report the solution at this place.
>
> Generating valid (for read.table) tab-delimited tables with Excel is 
> remarkably difficult - does anyone on this list have a better suggestion 
> of how to let users create these files (a) with a tool they like and 
> know and (b) in a way that more robustly reads into R?
>   
I don't think that there really is a better tool than Excel, at least 
nothing that is widely available. This might be one of the few 
situations where coming up with a GUI-like thing is actually worth the 
effort. It seems to me that the structure of the files that need to be 
generated for cellHTS is fairly stable and also that the workflow should 
be more or less standardized at this point of a screen. Any tool that 
allows you to basically enter arbitrary things without any control about 
structure or type will eventually cause read.table to crash, there's 
just too many factors that can be messed up.
I will try to get an overview over what is needed and think about a 
solution that doesn't involve too much nasty GUI programming and that is 
also portable over systems (bye bye to .NET...). The QT stuff seems to 
be very promising and Deepayan claims that things can be implemented 
fairly easily. The QT framework is GPL, so it could be wrapped in a 
standalone executable and if we wanted to we could even do things from 
within R.

bw,
Florian


> 	Thanks and best wishes
> 		 Wolfgang
>
> ------------------------------------------------------------------
> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
>
>
> dunicadj at tcd.ie scripsit:
>   
>> Hi all ,
>>
>> I have a problem when configuring my files in CellHTS2. Primarily, I get an
>> error concerning my ConfFile which says the following-
>>
>> Error in convertWellCoordinates(slog$Well, pdim(object)) :
>>   'x' must be either a character vector with alphanumeric well IDs (e.g. 'B03'
>> or c('B', '03'))
>>  or a vector of integers with position IDs within a plate (e.g. 27).
>>
>> My Plateconf.txt file looks like this, which to me seems the right format.
>> However, regardless of whether I specify each plate and well as below, or use
>> the compressed format shown in the cellHTS2 vignette I still get the same
>> error.
>>
>> Wells: 96
>> Plates: 18
>> Plate	Well	Content
>> 1	A01	Neg
>> 1	A02	Neg
>> 1	A03	Sample
>> 1	A04	Sample
>> 1	A05	Sample
>> 1	A06	Sample
>>
>> My only naïve idea is that while generating the tab delinated txt file using
>> exell that the final well descriptions are not recognised as alphanumeric by
>> cellHTS2. I have tried generating the file in notepad but with no success.
>> Is there some other way I should be generating the plateConf file? I have even
>> adapted the ConfFile from the KcViab example folder and stil get the same
>> error.
>> I have attached a copy of my ConfFile if necessary
>> Any help would be greatfully appreciated.
>>
>>
>>
>> Dara Dunican
>> Cell Signalling Group,
>> Institute of Molecular Medicine,
>> Trinity College Dublin,
>> Ireland
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
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>
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-- 
Florian Hahne, PhD
Computational Biology Program
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-3148
fhahne at fhcrc.org