[BioC] problem with GEOquery

[Sean Davis]

Thanks, Simon, for the report.  I'll certainly look into it.

However, you might want to take a look at GEOmetadb.  If there is
annotation that is missing from the database that GEOmetadb works with
(see the vignette), let us know and we can look at adding it, but I
think we capture pretty much all of the available GEO metadata for all
the platforms, datasets, series, and samples.  You can use SQL queries
to gather this information VERY quickly.  If you have questions about
using GEOmetadb, let me know.

Sean


On Thu, Jul 10, 2008 at 1:41 PM, Simon de Bernard
<simon.debernard at altrabio.com> wrote:
> Dear Sean,
>
> I used to be able to trim GEO soft files to get rid of the signal data (I'm
> only interested in the meta data and parsing the whole file takes forever
> for some datasets) using, for example:
>
> zcat GSE2109_family.soft.gz | grep '^[#^!]' > GSE2109.txt
>
> and then read the data with:
>
> meta <- getGEO(filename="GSE2109.txt")
>
> However, it does not work anymore:
>
> the above example gives me:
> Parsing....
> ^PLATFORM = GPL570
> Error in validObject(.Object) :
>  invalid class "GEODataTable" object: invalid object for slot "table" in
> class "GEODataTable": got class "factor", should be or extend class
> "data.frame"
>
> I tried to include part of the data with:
>
> zcat GSE2109_family.soft.gz | grep -A2 '^[#^!]' | grep -v "^--$" >
> GSE2109.txt
>
> But it doesn't work either:
> Parsing....
> ^PLATFORM = GPL570
> Error in read.table(file = file, header = header, sep = sep, quote = quote,
>  :
>  no lines available in input
> In addition: Warning messages:
> 1: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>  cols = 1 != length(data) = 16
>
> Is there some way to get it working again (or may be some completely other
> and more conventional way to get the meta data I'm not aware of)?
>
> Thanks in advance,
>
> Simon.
>
>> sessionInfo()
> R version 2.7.0 Patched (2008-06-02 r45823)
> x86_64-apple-darwin8.11.1
>
> locale:
> C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] GEOquery_2.5.3 RCurl_0.9-2    Biobase_2.0.1
>
>