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

Wolfgang Huber huber at ebi.ac.uk
Wed Feb 20 01:13:51 CET 2008

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?

	Thanks and best wishes

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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