cellHTS2 readPlateList
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@jose-garcia-bernardo-3639
Last seen 10.3 years ago
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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Florian Hahne ▴ 540
@florian-hahne-2471
Last seen 10.3 years ago
Hi Jose, without a little more information it is hard to diagnose your problem. Could you bundle up all your files and the code that produces the error into a zip archive and mail to me? And also attach the output of sessionInfo() The error message indicates that the files specified in platlist.txt can not be found in the folder dataPath, so you might want to make sure that this is correct. dir(dataPath) should list the content of that folder, and you might want to make sure that this matches with your entries in platelist.txt. Cheers, Florian On 25.08.2009, at 07:14, Jose Garcia-Bernardo wrote: > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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@manca-marco-path-3578
Last seen 10.3 years ago
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 ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ 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: marted? 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]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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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] Envoy??: mardi 25 ao?t 2009 16:18 ??: 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 ********************************************************************** ****** ***************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** ****** ***************************************** ________________________________________ 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: marted? 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]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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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] > Envoy? : mardi 25 ao?t 2009 16:18 > ? : 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 > > > ******************************************************************** ******** > ***************************************** > > This email and any files transmitted with it are confidential and solely for > the use of the intended recipient. > > It may contain material protected by privacy or attorney-client privilege. > If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received this > email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on > +31626441205 Dr Marco MANCA > > ******************************************************************** ******** > ***************************************** > > > ________________________________________ > 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: marted? 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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] Envoy??: mardi 25 ao?t 2009 17:56 ??: 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] > Envoy? : mardi 25 ao?t 2009 16:18 > ? : 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 > > > ********************************************************************** ****** > ***************************************** > > This email and any files transmitted with it are confidential and solely for > the use of the intended recipient. > > It may contain material protected by privacy or attorney-client privilege. > If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received this > email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on > +31626441205 Dr Marco MANCA > > ********************************************************************** ****** > ***************************************** > > > ________________________________________ > 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: marted? 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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] > Envoy? : mardi 25 ao?t 2009 17:56 > ? : 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] >> Envoy? : mardi 25 ao?t 2009 16:18 >> ? : 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 >> >> >> >> > ******************************************************************** ******** > >> ***************************************** >> >> This email and any files transmitted with it are confidential and solely >> > for > >> the use of the intended recipient. >> >> It may contain material protected by privacy or attorney-client privilege. >> If you are not the intended recipient or the person responsible for >> >> delivering to the intended recipient, be advised that you have received >> > this > >> email in error and that any use is STRICTLY PROHIBITED. >> >> If you have received this email in error please notify us by telephone on >> +31626441205 Dr Marco MANCA >> >> >> > ******************************************************************** ******** > >> ***************************************** >> >> >> ________________________________________ >> 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: marted? 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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >> >> > >
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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] > Envoy? : mardi 25 ao?t 2009 16:18 > ? : 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 > > > ******************************************************************** ******** > ***************************************** > > This email and any files transmitted with it are confidential and solely for > the use of the intended recipient. > > It may contain material protected by privacy or attorney-client privilege. > If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received this > email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on > +31626441205 Dr Marco MANCA > > ******************************************************************** ******** > ***************************************** > > > ________________________________________ > 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: marted? 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang ------------------------------------------------------- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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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] Envoy??: mardi 25 ao?t 2009 18:05 ??: 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] > Envoy? : mardi 25 ao?t 2009 16:18 > ? : 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 > > > ********************************************************************** ****** > ***************************************** > > This email and any files transmitted with it are confidential and solely for > the use of the intended recipient. > > It may contain material protected by privacy or attorney-client privilege. > If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received this > email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on > +31626441205 Dr Marco MANCA > > ********************************************************************** ****** > ***************************************** > > > ________________________________________ > 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: marted? 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang ------------------------------------------------------- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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@elin-axelsson-2940
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Hi Jose, are you sure your files are where your dataPath says the are ( "/Documents and Settings/.. Screen/in" ) ? how did you set the dataPath? best, Elin Jose Garcia-Bernardo wrote: > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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