
------ Forwarded Message
From: Sean Davis <sdavis2@mail.nih.gov>
Date: Fri, 13 Mar 2009 10:44:30 -0400
To: Wacek Kusnierczyk <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>
Cc: Jack Zhu <zhujack@mail.nih.gov>
Subject: Re: GEO metadata



On Fri, Mar 13, 2009 at 10:25 AM, Wacek Kusnierczyk
<Waclaw.Marcin.Kusnierczyk@idi.ntnu.no> wrote:
> Hi Jack and Sean (I've concatenated your two emails into one),
> 
> Jack Zhu wrote:
>> > Hi Wacek,
>> >
>> > Thanks for your interest in using GEOmetadb. I would give you more specific
>> > path if I knew a little bit more your tasks with GEO data since GEOmetadb
>> > provides several ways to find and retrieve GEO data. As a general approach,
>> > you can use GEOmetadb package with power of SQL command to find right GEO
>> > datasets and then use GEOquery package to download or get data into R
>> > environment.
>> >
> Thanks a lot for your prompt answer.
> 
> The issue I am dealing with is that I want to find data sets (or series)
> where there is an interesting expression profile for a small set of
> chosen genes, and then retrieve those data sets in toto.  So here the
> filter condition is (in addition to preliminary filtering by organism
> etc., easily done with GEOmetadb) the expression profile. 
> 
> 
> Now, to get at the expression profile, can I use GEOquery to get just
> profiles, or do I need to download whole data sets and only then examine
> profiles, possibly discarding large amounts of downloaded data?  As far
> as I can see, GEOquery allows me to download and parse whole experiment
> files;  what about individual gene profiles?

This is only available via Eutils or Entrez.  GEOquery downloads and parses
data into objects that work well with Bioconductor. 
 
> 
> Can I access the GEO db with an sql client directly?  I failed to find
> information on this.

No.  In fact, the data at GEO are not in a database.  Only the metadata,
etc., are in the database there. 
 
> 
> 
> Sean Davis wrote:
>> > Hi, Wacek.  Let me know if you have any problems using GEOquery.  Also,
>> feel
>> > free to ask questions like this on the Bioconductor mailing list, as then
>> > others benefit from the questions and answers.  As a matter of fact, would
>> > it be OK if Jack forwards his answer to the list?
>> >
>> >
> 
> Thanks for support.  I'm investigating the ways of using GEOquery for my
> tasks.  As far as I can see, it's very helpful.
> 
> It is ok to forward the exchange to the mailing lists where relevant.  I
> need to subscribe myself.
> 
> Cheers,
> vQ
> 
> 
>> > This is an example:
>> >
>> > ## example of finding all GSEs having 'breast cancer' in the summary:
>> >
>> >
>>> >> source("http://bioconductor.org/biocLite.R")
>>> >> biocLite("GEOmetadb")
>>> >> library(GEOmetadb)
>>> >> getSQLiteFile()
>>> >> con <- dbConnect(SQLite(), "GEOmetadb.sqlite")
>>> >> rs <- dbGetQuery(con, paste("select gse, title from gse where summary >>>
like
>>> >>
>> > '%breast cancer%' limit 5"))
>> >
>>> >> dbDisconnect(con)
>>> >>
>> >
>> > ## Using functions in GEOquery to download or parse data into R objects
>> > ## getGEO    Get a GEO object from NCBI or file
>> > ## getGEOfile    Download a file from GEO soft file to the local machine
>> > ## getGEOSuppFiles    Get Supplemental Files from GEO
>> > ## biocLite("GEOquery")
>> >
>> >
>>> >> library(GEOquery)
>>> >> myGSEMatrix <- getGEO(rs$gse[1], GSEMatrix = TRUE)
>>> >>
>> > ## using a loop to get multiple
>> >
>> > Hope this helps. Sean Davis might have more tips for you. Please let us
>> know
>> > if you have any questions.
>> >
>> > Jack
>> >
>> >
>> > On 3/13/09 7:17 AM, "Wacek Kusnierczyk"
>> > <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no> wrote:
>> >
>> >
>>> >> Dear Jack Zhu,
>>> >>
>>> >> I am using your excellent GEOmetadb Bioconductor package, it's very
>>> >> useful.
>>> >>
>>> >> I wonder whether you could hint me how I could access the GEO data --
>>> >> both data and metadata -- directly, if possible.  As you remarked
>>> >> yourself, using eutils is not always convenient, and the only
>>> >> programmatic access to the expression data I found is through
>>> >> downloading a file by ftp.
>>> >>
>>> >> My issue is that I'd like to scan through a large set of experiments
>>> >> where selected genes have interesting expression patterns, and only then
>>> >> retrieve the whole relevant data sets.  As far as I can see, eutils give
>>> >> access to the metadata only, and while it is possible to browse
>>> >> expression profiles on the GEO profiles site, they are not accessible
>>> >> programmatically.
>>> >>
>>> >> Best regards,
>>> >> Wacek
>>> >>
>>> >>
> 
> 
> --
> 
------------------------------------------------------------------------------>
-
> Wacek Kusnierczyk, MD PhD
> 
> Email: waku@idi.ntnu.no
> Phone: +47 73591875, +47 72574609
> 
> Department of Computer and Information Science (IDI)
> Faculty of Information Technology, Mathematics and Electrical Engineering
> (IME)
> Norwegian University of Science and Technology (NTNU)
> Sem Saelands vei 7, 7491 Trondheim, Norway
> Room itv303
> 
> Bioinformatics & Gene Regulation Group
> Department of Cancer Research and Molecular Medicine (IKM)
> Faculty of Medicine (DMF)
> Norwegian University of Science and Technology (NTNU)
> Laboratory Center, Erling Skjalgsons gt. 1, 7030 Trondheim, Norway
> Room 231.05.060
> 
> 
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> 



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