On Wed, May 12, 2010 at 2:46 AM, Assa Yeroslaviz <frymor@gmail.com> wrote:

> Good morning,
>
> I'll try to explain a bit further.
> I have a list of over 40,000 mouse genes which I would like to cluster,
> align etc. I have the list of expreession values as an excel file. In this
> file I have the GEO annotations as Probe IDs of the genes. I would like to
> add the GO Annotations Hugo Symbols (and so on, what's needed).


> But first I wanted to find out what kind of array are these annotations
> coming from. I tried to use GEOquery, but as far as I understood it only
> works one way GENE <- getGEO(). So I have had to look for the right GSE
> file, so I can download the Annotations and gene ID's.
> As I said I have found it at last.


If you have data that is from an unknown source, there will necessarily be
some forensics involved to determine what needs to be done.  If you have
data from GEO, though, then one will want to get the appropriate GEO
accession and proceed from there.  It is good to hear that you found what
you needed.


>
> What I wanted to know is whether there is a better, more efficient way of
> solving this problem. Is there a way in R of giving GEO annotations as an
> Input and getting other annotations as a result?
>

The way to do that is to use getGEO() to download the appropriate GPL.
After that, you can use any R tools you like to extract data from the
resulting object.  I'm not sure how that is inefficient,


>
> What about Biomart? could this works? I haven't tried ot yet, but I will
> now..
>
>
Biomart could work for some arrays, yes.  Also, you could use AnnotationDbi
to buid a custom annotation package.

Hope that helps.
Sean



> If you have any other Ideas, I would like to hear them.
>
> Assa
>
> On Tue, May 11, 2010 at 17:16, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
> >
> >
> > On Tue, May 11, 2010 at 11:01 AM, Assa Yeroslaviz <frymor@gmail.com
> >wrote:
> >
> >> well not exactly,
> >>
> >> I found first the soft file on the server before I found out what GSE
> File
> >> I
> >> need. :~)
> >> I found the GEOquery only later.
> >>
> >> What I didn't get there was how do i find what GSE i needed. Just by
> >> stating
> >> the A-52... Number didn't get me anywhere. I have had to look on the
> >> server
> >> which chip ahs these annotations ( i didn't even know if this is an
> >> Agilent
> >> or an affymetrix chip)
> >>
> >> Is there a way of making such a query using GEOquery?
> >> If i understood it correctly, GEOquery is only to get GEO-annotation
> from
> >> the server but not the other way around.
> >>
> >> Am i wrong?
> >>
> >
> > If you know the GPL you want, GEOquery can download it and put it into R
> > data structures.  If you are starting from a GSE (are you?), GEOquery
> will
> > download that AND the associated annotation automatically.
> >
> > If your use case is to start with a probe ID, that isn't something that
> GEO
> > was designed to deal with, at least as a download.  With a single probe,
> you
> > could, of course go here:
> >
> > http://www.ncbi.nlm.nih.gov/geo/
> >
> > Do a gene profile search and then from there you will have your GPL
> > annotation.
> >
> > Perhaps I'm not clear on what you are trying to do, though.  If you want
> > more input, could you clarify what you are trying to do (bigger picture)?
> >
> > Sean
> >
> >
> >
> >> On Tue, May 11, 2010 at 16:53, Sean Davis <sdavis2@mail.nih.gov> wrote:
> >>
> >> >
> >> >
> >> > On Tue, May 11, 2010 at 10:51 AM, Assa Yeroslaviz <frymor@gmail.com
> >> >wrote:
> >> >
> >> >> Hi Sean,
> >> >>
> >> >> Thankx for the answer, but I think I found a solution.
> >> >> I have for example the GEO name A_52_P431770
> >> >> it's from the mouse genome (GSE14293) and I wanted to have the gene
> >> >> symbols.
> >> >> But I downloaded the complete GSE file and will merge it with my gene
> >> >> list.
> >> >>
> >> >> If there are any other simpler /more efficient ideas, I would like to
> >> hear
> >> >> about them.
> >> >>
> >> >>
> >> > You are using GEOquery, correct?  (hint, hint....)
> >> >
> >> > Sean
> >> >
> >> >
> >> >>
> >> >> On Tue, May 11, 2010 at 16:47, Sean Davis <sdavis2@mail.nih.gov>
> >> wrote:
> >> >>
> >> >> >
> >> >> >
> >> >> > On Tue, May 11, 2010 at 10:08 AM, Assa Yeroslaviz <
> frymor@gmail.com
> >> >> >wrote:
> >> >> >
> >> >> >> Hello  everybody,
> >> >> >>
> >> >> >> Is there a way of converting GEO annotations to gene names?
> >> >> >> I have a list of GEO annotattions, but I would like to work with
> the
> >> >> >> "real"
> >> >> >> gene names.
> >> >> >> I was wondering whether there is a way of coverting a list of GEO
> >> >> >> annotation
> >> >> >> to its official (HUGO, NCBI, etc..) names and/or vice versa.
> >> >> >>
> >> >> >>
> >> >> > Hi, Assa.  You'll probably need to provide a concrete example.
>  "GEO
> >> >> > annotation" is not, unfortunately, a well-defined concept.
> >> >> >
> >> >> > Sean
> >> >> >
> >> >> >
> >> >>
> >> >>         [[alternative HTML version deleted]]
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> >> >
> >>
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