[BioC] Mapping annotation Data with GEO platform

[Sean Davis]

On Tue, Jun 10, 2008 at 4:20 PM, Wan Kyu Kim <wkimwkim at googlemail.com> wrote:
> Dear folks,
>
> I would like to link GEO platform ID with the annotation Data library.
> For example, "mgu74a" with "GPL81".
>
> Is there such information?

Yes, Wan.  We have done that in the GEOmetadb package.  Here is what
you can do to get the information

> library(GEOmetadb)
> getSQLiteFile()  # this is a 37Mb file and gets stored in the current directory
trying URL 'http://meltzerlab.nci.nih.gov/apps/geo/GEOmetadb.sqlite.gz'
Content type 'application/x-gzip' length 39155826 bytes (37.3 Mb)
opened URL
==================================================
downloaded 37.3 Mb

[1] "Unzipping..."
[1] "Metadata associate with downloaded file"
                name               value
1     schema version                 1.0
2 creation timestamp 2008-05-12 13:43:16
[1] "/tmp/GEOmetadb.sqlite"
> con <- dbConnect('SQLite','GEOmetadb.sqlite')
> gplToBioc <- dbGetQuery(con,'select gpl,bioc_package,title from gpl where bioc_package is not null')
> gplToBioc[1:3,] # just the first 3 rows of about 50 total
    gpl bioc_package                                            title
1 GPL32       mgu74a Affymetrix GeneChip Murine Genome U74A Version 1
2 GPL33       mgu74b Affymetrix GeneChip Murine Genome U74B Version 1
3 GPL34       mgu74c Affymetrix GeneChip Murine Genome U74C Version 1


Because this was done by hand, it is pretty affy-centric at this
point.  The columnDescriptions() function will give you information
about the columns in the various other tables that store all the GEO
metadata.

Hope that helps.
Sean