------ 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 > > ---------------------------------------------------------------------- --------> - > ------ End of Forwarded Message [[alternative HTML version deleted]]