[BioC] About ArrayExpress MAGE-TAB tools

[Sean Davis]

On Wed, Sep 24, 2008 at 11:05 AM, Jenny Drnevich <drnevich at illinois.edu> wrote:
> 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.

For read-only access, the public username and password are:

readonly
readonly

Sean


> 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
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu
>
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