[BioC] About ArrayExpress MAGE-TAB tools

[Jenny Drnevich]

Hi Wolfgang and Audry,

What's the status of the ArrayExpress package? I don't see it on the 
development branch yet, and I can't get into the svn repository - it 
wants a username and password.

Thanks,
Jenny

At 05:58 AM 6/11/2008, Wolfgang Huber wrote:

>Dear Li,
>
>to clarify: you can get the source of the package from the Bioconductor
>svn: See http://wiki.fhcrc.org/bioc/DeveloperPage and
>https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks
>
>If this means nothing to you, then please don't worry, and you could use
>the package once it is added to the list of packages for the build
>system, and then you will find it here:
>http://www.bioconductor.org/packages/2.3/bioc/
>
>If you are comfortable with svn and installing packages from source, we
>would be interested in your feedback.
>
>Best wishes
>  Wolfgang
>
>------------------------------------------------------------------
>Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
>
>11/06/2008 10:13 audrey scripsit
> > Hi LiGang,
> >
> > We are currently developing such a package. It is simply named
> > ArrayExpress and is currently on the Bioconductor svn but not on the
> > development branch yet. Hopefully it should be moved to the Bioconductor
> > development branch very soon but I still have some issues to fix before.
> > The ArrayExpress package takes an ArrayExpress experiment ID as an input
> > and creates an ExpressionSet, an AffyBatch or a NChannelSet as an output.
> >
> > Audrey
> >
> >
> > LiGang wrote:
> >> Hi, there,
> >>
> >> I want explore Microarray databases such as ArrayExpress and GEO using
> >> Bioconductor functionalities. For GEO there is the GEOquery package. Is
> >> there something similar for ArrayExpress?
> >>
> >>
> >> I have noted that in a PPT of "MAGE-TAB - a simple tab delimited
> >> format for
> >> describing microarray and other functional genomics experiments" (
> >> uhts.lbl.gov/images/4/4a/AlvisBrazma.ppt), the author mentioned that
> >> "Bioconductor module for reading in MAGE-TAB (beta release available at
> >> present)". Have this "Bioconductor module" publicly available and
> >> where can
> >> I find it? Thanks!
> >>
> >>
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
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ph: 217-244-7355
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e-mail: drnevich at illinois.edu