[BioC] cellHTS2 readPlateList

[Elin Axelsson]

Try if it works if you add .txt like:

Filename	Plate	Replicate
Plate1Replicate1.txt	1	1
Plate1Replicate2.txt	1	2
Plate2Replicate1.txt	2	1

as that's how you call your files in the data folder

best,
Elin

Jose Garcia-Bernardo wrote:
> Something like this:
>
> Filename	Plate	Replicate
> Plate1Replicate1	1	1
> Plate1Replicate2	1	2
> Plate2Replicate1	2	1
> Plate2Replicate2	2	2
> Plate3Replicate1	3	1
> Plate3Replicate2	3	2
> Plate4Replicate1	4	1
> Plate4Replicate2	4	2
>
> Down to 175 plates in two replicates each.
>
> -----Message d'origine-----
> De : Elin Axelsson [mailto:elin at ebi.ac.uk] 
> Envoyé : mardi 25 août 2009 17:56
> À : Jose Garcia-Bernardo
> Cc : bioconductor at stat.math.ethz.ch
> Objet : Re: [BioC] cellHTS2 readPlateList
>
> hmm, maybe a stupid question but how does your "platelist.txt" look?
>
> Elin
>
> Jose Garcia-Bernardo wrote:
>   
>> Thank you to both for your quick replies!
>>
>> Yes, indeed are all files in the folder of the specified path and I
>>     
> changed
>   
>> twice the path to make sure it was the right one. However I still get the
>> same message. These are the first few lines of the code that I wrote:
>>
>>   
>>     
>>> RasV12="Bioconductordata"
>>> dataPath=('C:/Documents\ and Settings/....../Bioconductordata')
>>> dataPath
>>>     
>>>       
>> [1] "C:/Documents and Settings/......./Bioconductordata"
>>   
>>     
>>> rev(dir(dataPath))[1:351]
>>>     
>>>       
>>   [1] "platelist.txt"          "Plateconf.txt"
>> "Plate9Replicate2.txt"   "Plate9Replicate1.txt"   "Plate99Replicate2.txt"
>> "Plate99Replicate1.txt" 
>>   [7] "Plate98Replicate2.txt"  "Plate98Replicate1.txt"
>> "Plate97Replicate2.txt"  "Plate97Replicate1.txt"  "Plate96Replicate2.txt"
>> "Plate96Replicate1.txt" 
>>  [13] "Plate95Replicate2.txt"  "Plate95Replicate1.txt"
>> "Plate94Replicate2.txt"  "Plate94Replicate1.txt"  "Plate93Replicate2.txt"
>> "Plate93Replicate1.txt" 
>>  [19] "Plate92Replicate2.txt"  "Plate92Replicate1.txt"
>> "Plate91Replicate2.txt"  "Plate91Replicate1.txt"  "Plate90Replicate2.txt"
>> "Plate90Replicate1.txt" 
>>  [25] "Plate8Replicate2.txt"   "Plate8Replicate1.txt"
>> "Plate89Replicate2.txt"  "Plate89Replicate1.txt"  "Plate88Replicate2.txt"
>> "Plate88Replicate1.txt"
>>
>>
>>
>> And then I try to read into the object as follows:
>>
>>   
>>     
>>> x=readPlateList("platelist.txt",
>>>     
>>>       
>> + name=RasV12,
>> + path=dataPath)
>> Erreur dans readPlateList("platelist.txt", name = RasV12, path = dataPath)
>>     
> :
>   
>>   None of the files were found in the given 'path': C:/Documents and
>> Settings/Natalia Araujo/Bureau/Bioconductordata
>>
>> Is the problem perhaps related to the experimentName?
>>
>>
>> Thank you!
>>
>> Jose
>>
>>
>> -----Message d'origine-----
>> De : Manca Marco (PATH) [mailto:m.manca at path.unimaas.nl] 
>> Envoyé : mardi 25 août 2009 16:18
>> À : Jose Garcia-Bernardo; bioconductor at stat.math.ethz.ch
>> Objet : R: [BioC] cellHTS2 readPlateList
>>
>>
>>
>> Dear Jose
>>
>> are you sure your platelist.txt file (and all the other relevant files as
>> well) is in your working directory? I assume you are using R for windows
>>     
> (I
>   
>> guess by the path you are getting in the error message) thus you may
>>     
> easily
>   
>> check that by going into "File" -> "Change dir..." and when prompted to
>> select your desired working directory go for the path your files are in...
>>
>> I hope this helps.
>>
>> Best regards,
>> Marco
>>
>>
>>
>>     
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>>
>> ________________________________________
>> Da: bioconductor-bounces at stat.math.ethz.ch
>> [bioconductor-bounces at stat.math.ethz.ch] per conto di Jose Garcia-Bernardo
>> [jose.garcia at vjf.cnrs.fr]
>> Inviato: martedì 25 agosto 2009 16.14
>> A: bioconductor at stat.math.ethz.ch
>> Oggetto: [BioC] cellHTS2 readPlateList
>>
>> Dear all
>>
>> A very basic question from a complete beginner.
>>
>>
>>
>> I'm getting an error message every time I try to read the data into the
>> object x:
>>
>>
>>
>> Erreur dans readPlateList("platelist.txt", name = experimentName, path =
>> dataPath) :
>>
>>   None of the files were found in the given 'path': C:/Documents and
>> Settings/.. Screen/in
>>
>>
>>
>> When using the following (standard) code:
>>
>>
>>
>>   
>>     
>>> x <- readPlateList("platelist.txt",
>>>     
>>>       
>> + name=experimentName,
>>
>> + path=dataPath)
>>
>>
>>
>> All measurement files and the platelist file are in the same folder within
>> the same directory. Not sure if it's a fundamental problem or just a
>>     
> simple
>   
>> bug in the code (apologies for this).
>>
>>
>>
>> Any help will be very much appreciated
>>
>>
>>
>> Jose
>>
>>
>>         [[alternative HTML version deleted]]
>>
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