[BioC] Agilent MAGE-ML

Wolfgang Huber huber at ebi.ac.uk
Fri Aug 22 15:51:25 CEST 2008

Hi Gabriele,

I have not yet had to use this, but there is a MAGE-ML to MAGE-TAB
converter here:
and reading MAGE-TAB should be reasonably straightforward if you know a
little bit of R and read.table.

Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

20/08/2008 17:34 Martin Morgan scripsit
> 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.
> http://www.ebi.ac.uk/microarray/doc/software/schema/MAGE/MAGE.htm
> 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
> read.maimages.
>> 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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