Question: Agilent MAGE-ML
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11.1 years ago by
gabriele bucci10 wrote:
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. My questions are: 1) when talking in general about 'Agilent .txt files' were actually talking about MAGE files? 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
rmageml genespring process • 674 views
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modified 11.1 years ago by Martin Morgan ♦♦ 23k • written 11.1 years ago by gabriele bucci10
Answer: Agilent MAGE-ML
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11.1 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:
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' were 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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
ADD COMMENTlink written 11.1 years ago by Martin Morgan ♦♦ 23k
Hi Gabriele, I have not yet had to use this, but there is a MAGE-ML to MAGE-TAB converter here: http://www.mged.org/mage-tab/tools.html and reading MAGE-TAB should be reasonably straightforward if you know a little bit of R and read.table. Best wishes Wolfgang ------------------------------------------------------------------ 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLYlink written 11.1 years ago by Wolfgang Huber13k
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