[BioC] Normalization of array data from GEO repository

[Aleš Maver]

Great! thank you for all the info and useful advice regarding
arrayQualityMetrics and ArrayExpress!

Regards,
Ales

2009/7/8 Joern Toedling <Joern.Toedling at curie.fr>
>
> Hello,
>
> 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.
>
> Regards,
> Joern
>
>
> 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
>



--
Aleš Maver
Ales.Maver at gmail.com