[BioC] cellHTS2 readPlateList

Jose Garcia-Bernardo jose.garcia at vjf.cnrs.fr
Tue Aug 25 19:00:41 CEST 2009 

I think I found the problem! 

Bioconductordata: found data in 16 x 24 (384 well) format.

Read 350 plates.

cellHTS (storageMode: lockedEnvironment)
assayData: 67200 features, 2 samples 
  element names: Channel 1 
phenoData
  sampleNames: 1, 2
  varLabels and varMetadata description:
    replicate: Replicate number
    assay: Biological assay
  additional varMetadata: channel
featureData
  featureNames: 1, 2, ..., 67200  (67200 total)
  fvarLabels and fvarMetadata description:
    plate: Plate number
    well: Well ID
    controlStatus: Well annotation
experimentData: use 'experimentData(object)'
state:  configured = FALSE
        normalized = FALSE
        scored = FALSE
        annotated = FALSE 
Number of plates: 175  
Plate dimension: nrow = 16, ncol = 24 
Number of batches: 1 
>

There was another txt file in the same folder named 'index', containing
exactly the same information as in my platelist file. I changed if for this
one and fixed the problem. Does this help to explain it? 

Index file as follows:

Filename	Plate	Replicate
Plate1Replicate1.txt	1	1
Plate1Replicate2.txt	1	2
Plate2Replicate1.txt	2	1
Plate2Replicate2.txt	2	2


Platelist as follows:


Filename	Plate	Replicate
Plate1Replicate1.txt	1	1
Plate1Replicate2.txt	1	2
Plate2Replicate1.txt	2	1
Plate2Replicate2.txt	2	2
Plate3Replicate1.txt	3	1
Plate3Replicate2.txt	3	2

I don't see any difference... 


Thank you very much for your help and time.

Jose







-----Message d'origine-----
De : Wolfgang Huber [mailto:whuber at embl.de] 
Envoyé : mardi 25 août 2009 18:05
À : Jose Garcia-Bernardo
Cc : bioconductor at stat.math.ethz.ch
Objet : Re: [BioC] cellHTS2 readPlateList

Dear Jose,

Your problem could be that you use different spelling of the filenames 
in platelist.txt compared to those in that directory; or funny special 
characters. Can you:

1. Show us the content of your 'plateList.txt' file?

2. (This is slightly advanced, but perhaps you can manage:) Run
  options(error=recover)
before calling readPlateList, and then when the error occurs, you get a 
menu: "Enter a frame number, or 0 to exit". Please enter the number that 
corresponds to the readPlateList function, then, in the debugger prompt, 
type:
   pd$Filename
   dfiles
To exit the debugger, type "Q".

3. Provide us with the output of sessionInfo()


	Best wishes
	Wolfgang


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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-- 

Best wishes
      Wolfgang

-------------------------------------------------------
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber

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