Thanks Vincent, I'm actually updating R as we speak - so thanks for letting me know that I shouldn't expect this to work. Please let me know if you stumble upon a possible cause. Best, Mikhail On Sun, Nov 27, 2011 at 10:07 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > 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 at="" 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/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. >> >> _______________________________________________ >> 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 > >

Hi Mikhail, Thank you for your email. The index files containing the names of zip files to be downloaded have been changed in the database so I have now adapted the code to handle this new version. In ArrayExpress 1.15.1 in the devel branch, it should now work. I am waiting to test it a little bit more before updating also the release version of the package. Please let me know if this is better or if you have additional feedback in the next couple of days, it would be very useful so do not hesitate! Thanks and best wishes, Audrey On Sun, Nov 27, 2011 at 11:41 PM, Mikhail Spivakov <spivakov@ebi.ac.uk>wrote: > Thanks Vincent, I'm actually updating R as we speak - so thanks for > letting me know that I shouldn't expect this to work. > Please let me know if you stumble upon a possible cause. > > Best, > Mikhail > > > On Sun, Nov 27, 2011 at 10:07 PM, Vincent Carey > <stvjc@channing.harvard.edu> wrote: > > 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 > > > > > > _______________________________________________ > 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]]