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!
kind regards,
Yuan
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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