[BioC] Agilent MAGE-ML

Martin Morgan mtmorgan at fhcrc.org
Wed Aug 20 18:34:22 CEST 2008

Hi Gabriele --

A little slow on the response, but I wanted to provide a couple of
not-very-complete suggestions. 

gabriele bucci <gabriele.bucci at ifom-ieo-campus.it> writes:

> Dear List,
> some external collaborators gave us the results of an expression
> profiling over tumor samples.
> The experiment is a dye swap, and they are using a rosetta resolver
> platform.
> The chips used were Agilent two-colors custom arrays and the data
> which were provided to us are in the form of ".mage" files.
> So I suppose these files are actually a MAGE-ML files.
> Except for the package 'RMAGEML' which run only under a Linux R
> environment (I'm working under winXP), I was not able to find a
> Bioconductor solution to read and process this MAGE-ML files.

'AffyCompatible' will parse MAGE files; unfortunately, it requires a
version of the XML package (e.g., 1.95-3) that is different from the
one available by default. Try

> install.packages('XML', repos='http://www.omegahat.org/R')
> source('http://bioconductor.org/biocLite.R')
> biocLite('AffyCompatible')
> library(AffyCompatible)
> example(readMage)

You'll end up with a complicated object that you can traverse (use the
names suggested by the display of the object, with vector-like
elements suggested by () and accessible with [[) to retrieve relevant
information; there is no easy way to convert this to, say, an
ExpressionSet, and the MAGE model is horrendously complicated.


The help page for readMage also points to readXml, which will be a
more efficient way to retrieve information once you know what it is
that you want. There are useful vignettes in the package, too.

A further complication is that Affy used MAGE for sample attribute
description, not for storing expression data; Rosetta Resolver might
well do the same thing but I have no direct experience. Also MAGE
implementations are not always compliant with the standard, so the
MAGE in AffyCompatible may differ in obscure ways from the MAGE used
by Rosetta.

> My questions are:
> 1) when talking in general about 'Agilent .txt files'  we`re actually
> talking about MAGE files?

If you have Agilent .txt files, then probably this is the data that
will be most useful in the analysis, e.g., using limma's

> 2) is there a way to port RMAGEML on R under windows?
> 3) alternative solutions.
> I will appreciate any kind of suggestion and comment, if you have some.
> My Best wishes,
> Gabriele
> PS. I've tried also with Partek and GeneSpring GX (7.3) without success...
> -- 
> Gabriele Bucci, PhD 
> COGENTECH  -Consortium for Genomic Technologies- 
> Via Adamello 16 20139 Milano  -Italia- 
> Tel.    +39 02 94375134 Fax.    +39 02 94375991
> gabriele.bucci at ifom-ieo-campus.it
> service-array at ifom-ieo-campus.it
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

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