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/GSM90393.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90378.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90405.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90387.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90356.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90334.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90361.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90368.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90332.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90327.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90314.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90392.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90320.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90360.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90333.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90389.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90357.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90337.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90401.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90379.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90399.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90315.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90309.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90347.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90308.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90375.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90380.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90344.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90321.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90394.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90348.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90328.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90403.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90388.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90346.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90383.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90310.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90335.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90395.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90365.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90364.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90331.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90339.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90325.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90374.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90367.CEL
> >>
> >>
> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90382.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
> >
> >
>
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