Entering edit mode
Hello,
If I execute the following three lines:
library('GEOquery')
gds <- getGEO('GSE2034')
eset <- GDS2eSet(gds)
I get the following error message after the call to GDS2eSet():
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "Table", for
signature "GSE"
I'm using R version 2.6.0 and GEOquery version 2.2.0 (see details
below), but it
also happens with R version 2.5.2 and GEOquery version 2.0.6.
Any help would be appreciated.
Thanks.
-Ben
----------------------------------------------------------------------
-----
> eset <- GDS2eSet(gds)
trying URL
'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL96&for
m=text&vie
w=full'
Content type 'geo/text' length unknown
opened URL
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
(many such lines deleted)
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
...
downloaded 23.4 Mb
File stored at:
/tmp/Rtmpf1P0of/GPL96.soft
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "Table", for
signature "GSE"
> version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 6.0
year 2007
month 10
day 03
svn rev 43063
language R
version.string R version 2.6.0 (2007-10-03)
> packageDescription('GEOquery')
Package: GEOquery
Type: Package
Title: Get data from NCBI Gene Expression Omnibus (GEO)
Version: 2.2.0
Date: 2007-09-24
Author: Sean Davis <sdavis2 at="" mail.nih.gov="">
Maintainer: Sean Davis <sdavis2 at="" mail.nih.gov="">
Depends: methods,Biobase,RCurl
Suggests: limma
biocViews: Microarray, DataImport, OneChannel, TwoChannel, SAGE
Description: The NCBI Gene Expression Omnibus (GEO) is a public
repository of microarray data (>150,000 experiments). Given
the rich and varied nature of these data, it is only natural
to
want to apply BioConductor tools to these data. GEOquery is
the bridge between GEO and BioConductor.
License: GPL version 2
Packaged: Wed Oct 3 14:31:57 2007; biocbuild
Built: R 2.6.0; ; 2007-11-05 16:42:50; unix
-- File: /home/bwittner/R-2.6.0/library/GEOquery/DESCRIPTION
>
The information transmitted in this electronic
communica...{{dropped:8}}