Dear folks, I would like to link GEO platform ID with the annotation Data library. For example, "mgu74a" with "GPL81". Is there such information? Doing it manually looks not very fun to do! wan [[alternative HTML version deleted]]

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