On Wed, Sep 1, 2010 at 7:39 AM, Yuan Hao <yuan.x.hao@gmail.com> wrote:

> Dear List,
>
> I want to get all the Affymetrix datasets (Human) from GEO and then group
> them according to different types of chips, like hgu133A, hgu133plus2, etc.
> so that I could know how many datasets available for each type of chips.
>
> I looked at the GEOquery package in R/Bioconductor. There are a
> 'manufacturer' and a 'Title' field in the GEO Platform record which might be
> useful for my purpose, but I didn't manage to figure out how to get all the
> Platform records into R workspace first. In the package vignette, it always
> deals with a single record by giving a specific accession number such as
> GPLxxxx, but how could I get all the records meet my criteria? Could you
> kindly provide some help on this? Thank you very much in advance!
>
>
Hi, Yuan.

Take a look at the GEOmetadb package.  There is an example almost matching
the one you describe.  To get you started, install the GEOmetadb package and
then try:

library(GEOmetadb)
fn = getSQLiteFile()
con <- dbConnect(SQLite(), fn)
rs <- dbGetQuery(con, paste("select gpl.bioc_package,gsm.gpl,count(gsm)",
        "from gsm join gpl on gsm.gpl=gpl.gpl",
        "where gpl.manufacturer='Affymetrix'",
        "group by gpl.bioc_package,gsm.gpl"))
rs

Sean

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