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
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:
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>
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
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
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]]
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]]
>
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