[BioC] ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"

[Mikhail Spivakov [guest]]

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           


--
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