ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"
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@guest-user-4897
Last seen 6.6 years ago
Hi everyone, I've tried importing two different datasets using ArrayExpress and unfortunately I'm getting the same error: unable to find an inherited method for function "experimentData", for signature "try-error". Could you please advice what might be causing the problem? The R output is pasted below. Many thanks! Mikhail > library(ArrayExpress) > wang = ArrayExpress( input = "E-GEOD-3960") # also tried "E-GEOD-27608" trying URL 'http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-3960/index.html' Content type 'text/html;charset=UTF-8' length unknown opened URL ........ downloaded 9082 bytes trying URL 'http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-3960/E-GEOD-3960.raw.1.zip' Content type 'application/zip' length 156512666 bytes (149.3 Mb) opened URL ================================================ downloaded 149.3 Mb Read 1 item trying URL 'http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-3960/E-GEOD-3960.sdrf.txt' Content type 'text/plain' length 76290 bytes (74 Kb) opened URL ================================================== downloaded 74 Kb trying URL 'http://www.ebi.ac.uk/microarray- as/ae/files/A-AFFY-1/A-AFFY-1.adf.txt' Content type 'text/plain' length 1547751 bytes (1.5 Mb) opened URL ================================================== downloaded 1.5 Mb trying URL 'http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-3960/E-GEOD-3960.idf.txt' Content type 'text/plain' length 4279 bytes opened URL ================================================== downloaded 4279 bytes Error : the following are not valid files: /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM9 0393.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 378.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 405.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 387.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 356.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 334.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 361.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 368.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 332.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 327.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 314.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 392.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 320.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 360.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 333.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 389.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 357.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 337.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 401.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 379.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 399.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 315.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 309.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 347.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 308.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 375.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 380.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 344.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 321.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 394.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 348.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 328.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 403.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 388.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 346.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 383.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 310.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 335.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 395.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 365.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 364.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 331.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 339.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 325.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 374.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 367.CEL /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 382.CEL Read 49 items Error in function (classes, fdef, mtable) : unable to find an inherited method for function "experimentData", for signature "try-error" Warning message: In AB(i = 1, files, path, ph, adr, adf, idf) : Cannot attach experimentData -- Mikhail Spivakov, PhD European Bioinformatics Institute -- output of sessionInfo(): R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.25.3 ArrayExpress_1.8.0 Biobase_2.7.6 loaded via a namespace (and not attached): [1] affyio_1.15.2 limma_3.3.21 preprocessCore_1.9.0 [4] XML_3.1-0 -- Sent via the guest posting facility at bioconductor.org.
ArrayExpress ArrayExpress • 799 views
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@vincent-j-carey-jr-4
Last seen 6 days ago
United States
You really should update your R, but this is confirmed with current R 2.14 -- I don't know what is happening, there are many possible causes, and I will investigate a little, but others closer to this package should have a look. Read 49 items Error in function (classes, fdef, mtable) : unable to find an inherited method for function "experimentData", for signature "try-error" Warning message: In AB(i = 1, files, path, ph, adr, adf, idf) : Cannot attach experimentData > sessionInfo() R version 2.14.0 Patched (2011-11-09 r57622) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.iso88591 LC_NUMERIC=C [3] LC_TIME=en_US.iso88591 LC_COLLATE=en_US.iso88591 [5] LC_MONETARY=en_US.iso88591 LC_MESSAGES=en_US.iso88591 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] ArrayExpress_1.14.0 Biobase_2.14.0 weaver_1.20.0 [4] codetools_0.2-8 digest_0.5.1 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] affy_1.32.0 affyio_1.22.0 limma_3.10.0 [4] preprocessCore_1.16.0 XML_3.4-3 zlibbioc_1.0.0 On Sun, Nov 27, 2011 at 6:07 AM, Mikhail Spivakov [guest] < guest@bioconductor.org> wrote: > > Hi everyone, > > I've tried importing two different datasets using ArrayExpress and > unfortunately I'm getting the same error: unable to find an inherited > method for function "experimentData", for signature "try-error". > > Could you please advice what might be causing the problem? The R output is > pasted below. > > Many thanks! > Mikhail > > > library(ArrayExpress) > > wang = ArrayExpress( input = "E-GEOD-3960") # also tried "E-GEOD-27608" > trying URL ' > http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-3960/index.html' > Content type 'text/html;charset=UTF-8' length unknown > opened URL > ........ > downloaded 9082 bytes > > trying URL ' > http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-3960/E-GEOD-3960.raw.1.zip > ' > Content type 'application/zip' length 156512666 bytes (149.3 Mb) > opened URL > ================================================ > downloaded 149.3 Mb > > Read 1 item > trying URL ' > http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-3960/E-GEOD-3960.sdrf.txt > ' > Content type 'text/plain' length 76290 bytes (74 Kb) > opened URL > ================================================== > downloaded 74 Kb > > trying URL ' > http://www.ebi.ac.uk/microarray- as/ae/files/A-AFFY-1/A-AFFY-1.adf.txt' > Content type 'text/plain' length 1547751 bytes (1.5 Mb) > opened URL > ================================================== > downloaded 1.5 Mb > > trying URL ' > http://www.ebi.ac.uk/microarray- as/ae/files/E-GEOD-3960/E-GEOD-3960.idf.txt > ' > Content type 'text/plain' length 4279 bytes > opened URL > ================================================== > downloaded 4279 bytes > > Error : the following are not valid files: > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90 393.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 78.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM904 05.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 87.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 56.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 34.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 61.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 68.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 32.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 27.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 14.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 92.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 20.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 60.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 33.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 89.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 57.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 37.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM904 01.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 79.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 99.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 15.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 09.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 47.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 08.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 75.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 80.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 44.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 21.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 94.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 48.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 28.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM904 03.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 88.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 46.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 83.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 10.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 35.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 95.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 65.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 64.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 31.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 39.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 25.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 74.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 67.CEL > > /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM903 82.CEL > Read 49 items > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "experimentData", for > signature "try-error" > Warning message: > In AB(i = 1, files, path, ph, adr, adf, idf) : Cannot attach experimentData > > > -- > Mikhail Spivakov, PhD > European Bioinformatics Institute > > -- output of sessionInfo(): > > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.25.3 ArrayExpress_1.8.0 Biobase_2.7.6 > > loaded via a namespace (and not attached): > [1] affyio_1.15.2 limma_3.3.21 preprocessCore_1.9.0 > [4] XML_3.1-0 > > > -- > 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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