GEO annotation
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@roumyana-yordanova-2681
Last seen 10.2 years ago
Hi, Is there a package in R that downloads any available annotation (e.g. cancer type, time points, dose, etc.. for each sample) in the GSE series. Thank you. Roumyana
Annotation DOSE Annotation DOSE • 1.7k views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.3 years ago
United States
Roumyana Yordanova wrote: > Hi, > > Is there a package in R that downloads any available annotation (e.g. > cancer type, time points, dose, etc.. for each sample) in the GSE > series. > Thank you. > > Roumyana > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > Perhaps you want something like this? Package: GEOmetadb Type: Package Title: A compilation of metadata from NCBI GEO Version: 1.1.1 Date: 2008-04-03 Depends: GEOquery,RSQLite Author: Jack Zhu and Sean Davis Maintainer: Jack Zhu <zhujack at="" mail.nih.gov=""> biocViews: Infrastructure Description: The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. URL: http://meltzerlab.nci.nih.gov/apps/geo License: Artistic-2.0 Marc
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@sean-davis-490
Last seen 3 months ago
United States
On Wed, Jun 18, 2008 at 11:13 AM, Roumyana Yordanova <roumyana.yordanova at="" bms.com=""> wrote: > Hi, > > Is there a package in R that downloads any available annotation (e.g. cancer > type, time points, dose, etc.. for each sample) in the GSE series. Hi, Roumyana. If you need the information for a single GSE, you can look at the GEOquery package. If you want this for many (or all) data in GEO, look at the GEOmetadb package. Note that, in general, GEO does not curate the annotation and it is often not in a computable form. If you need more details, you could supply a little bit more detail about what you want to do. Sean
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Thanks. I need class information that can be used in ANOVA type analysis. GSE annotation is not well structured as you mentioned. GDS have some curated annotation that can be extracted with GEOquery. However, the latest GDS is from last year. Any ideas if GDS will be continued? Roumyana Sean Davis wrote: >On Wed, Jun 18, 2008 at 11:13 AM, Roumyana Yordanova ><roumyana.yordanova@bms.com> wrote: > > >>Hi, >> >>Is there a package in R that downloads any available annotation (e.g. cancer >>type, time points, dose, etc.. for each sample) in the GSE series. >> >> > >Hi, Roumyana. > >If you need the information for a single GSE, you can look at the >GEOquery package. If you want this for many (or all) data in GEO, >look at the GEOmetadb package. Note that, in general, GEO does not >curate the annotation and it is often not in a computable form. If >you need more details, you could supply a little bit more detail about >what you want to do. > >Sean > > > [[alternative HTML version deleted]]
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On Mon, Jun 23, 2008 at 10:46 AM, Roumyana Yordanova <roumyana.yordanova at="" bms.com=""> wrote: > Thanks. I need class information that can be used in ANOVA type analysis. > GSE annotation is not well structured as you mentioned. > GDS have some curated annotation that can be extracted with GEOquery. > However, the latest GDS is from last year. Any ideas if GDS will be > continued? I have not heard that GDS will not be continued, but your best bet is to email NCBI GEO directly for those questions. > > Sean Davis wrote: > >>On Wed, Jun 18, 2008 at 11:13 AM, Roumyana Yordanova >><roumyana.yordanova at="" bms.com=""> wrote: >> >> >>>Hi, >>> >>>Is there a package in R that downloads any available annotation (e.g. cancer >>>type, time points, dose, etc.. for each sample) in the GSE series. >>> >>> >> >>Hi, Roumyana. >> >>If you need the information for a single GSE, you can look at the >>GEOquery package. If you want this for many (or all) data in GEO, >>look at the GEOmetadb package. Note that, in general, GEO does not >>curate the annotation and it is often not in a computable form. If >>you need more details, you could supply a little bit more detail about >>what you want to do. >> >>Sean >> >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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