[BioC] Normalization of array data from GEO repository

Joern Toedling Joern.Toedling at curie.fr
Wed Jul 8 12:16:08 CEST 2009


just a small addendum: you may also want to have a look at the ArrayExpress
package which allows the user to retrieve data sets from the ArrayExpress
database at EBI and returns the data in form of an AffyBatch, NChannelSet,
RGList or the like. Since GEO and ArrayExpress are regularly synchronized, you
may be able to find your data sets of interest there as well.


On Tue, 7 Jul 2009 13:59:19 -0400, Steve Lianoglou wrote
> Hi,
> On Jul 7, 2009, at 5:38 AM, [WINDOWS-1252?]Aleš Maver wrote:
> > Hi all,
> > I have obtained several GEO Series (GSE) entries from GEO repository  
> > using
> > getGEO function (GEOquery package).
> > Data obtained in this manner is stored in ExpressionSet class. The  
> > problem
> > is I don't know how to perform quality control analyses and  
> > normalization
> > procedures on ExpressionSet data, because functions like expresso  
> > (affy
> > package) work only on AffyBatch classes. Is there anything I am  
> > missing?
> Sorry, I've never used the GEOquery package before, so I can't speak 
>  much to that, but I'd be surprised if there isn't an option to 
> return  your results as an AffyBatch object, because I'd dare say 
> that you can  get most of the data from geo in its raw format (eg, 
> CEL file or  whatever).
> > And- does anyone know whether data in GEO repository is already  
> > normalised
> > or not?
> It depends, sometimes you aren't given the raw files: sometimes the  
> data is from a custom array, or I've also seen some datasets 
> provided  in the post-processed form (already MAS5 normalized, for 
> example), but  it's been my experience that you can get the raw data 
> for most of the  experiments you find there.
> Also, for array quality assessment, look into the 
> arrayQualityMetrics  package:
> http://www.bioconductor.org/packages/release/bioc/html/arrayQualityMetrics.html
> Hope that helps,
> -steve

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