Can\'t read canine CEL file with ReadAffy()
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@guest-user-4897
Last seen 8.3 years ago
Dear R helpers, I would like to note in the first place that I'm very naive to R. So I must apologize you all in advance if my problem is too simple. Hope you will accept my apology. I can't read CEL files of canine bone cancers with 'ReadAffy()'. Would you please suggest me what happens and what I should try next? R shows me this error > ReadAffy() Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : Cel file D:/Canine Osteosarcoma/GSM596543.CEL does not seem to have the correct dimensions Best Regards, Kaj -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Thai_Thailand.874 LC_CTYPE=Thai_Thailand.874 [3] LC_MONETARY=Thai_Thailand.874 LC_NUMERIC=C [5] LC_TIME=Thai_Thailand.874 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 [4] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.
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@james-w-macdonald-5106
Last seen 1 minute ago
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Hi Kaj, You can try two things. First, check to see if this is the first file that you are trying to read. If so, there might have been a problem when you downloaded, so you might try re-downloading. Second, if it is not the first file, you might have a non-canine file in the bunch. You could try moving it to its own directory, read it in alone using ReadAffy() and then see what kind of celfile it is. Best, Jim On 3/17/13 6:25 AM, Kaj Chokeshaiusaha [guest] wrote: > Dear R helpers, > > I would like to note in the first place that I'm very naive to R. So I must apologize you all in advance if my problem is too simple. Hope you will accept my apology. > > I can't read CEL files of canine bone cancers with 'ReadAffy()'. > Would you please suggest me what happens and what I should try next? > R shows me this error > >> ReadAffy() > Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : > Cel file D:/Canine Osteosarcoma/GSM596543.CEL does not seem to have the correct dimensions > > Best Regards, > Kaj > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Thai_Thailand.874 LC_CTYPE=Thai_Thailand.874 > [3] LC_MONETARY=Thai_Thailand.874 LC_NUMERIC=C > [5] LC_TIME=Thai_Thailand.874 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 > [4] zlibbioc_1.4.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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@kaj-chokeshaiusaha-5769
Last seen 8.3 years ago
Dear James, Thank you very much. I will try what you suggest. Best regards, Kaj -----Original Message----- From: "James W. MacDonald" <jmacdon@uw.edu> Sent: ‎19/‎3/‎2013 3:07 To: "Kaj Chokeshaiusaha [guest]" <guest@bioconductor.org> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>; "kajkajkajkajkaj@gmail.com" <kajkajkajkajkaj@gmail.com>; "affy Maintainer" <rafa@jhu.edu> Subject: Re: [BioC] Can\'t read canine CEL file with ReadAffy() Hi Kaj, You can try two things. First, check to see if this is the first file that you are trying to read. If so, there might have been a problem when you downloaded, so you might try re-downloading. Second, if it is not the first file, you might have a non-canine file in the bunch. You could try moving it to its own directory, read it in alone using ReadAffy() and then see what kind of celfile it is. Best, Jim On 3/17/13 6:25 AM, Kaj Chokeshaiusaha [guest] wrote: > Dear R helpers, > > I would like to note in the first place that I'm very naive to R. So I must apologize you all in advance if my problem is too simple. Hope you will accept my apology. > > I can't read CEL files of canine bone cancers with 'ReadAffy()'. > Would you please suggest me what happens and what I should try next? > R shows me this error > >> ReadAffy() > Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : > Cel file D:/Canine Osteosarcoma/GSM596543.CEL does not seem to have the correct dimensions > > Best Regards, > Kaj > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Thai_Thailand.874 LC_CTYPE=Thai_Thailand.874 > [3] LC_MONETARY=Thai_Thailand.874 LC_NUMERIC=C > [5] LC_TIME=Thai_Thailand.874 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 > [4] zlibbioc_1.4.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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