CMA help
1
0
Entering edit mode
Clara Pons ▴ 30
@clara-pons-4673
Last seen 9.6 years ago
Hi to all, I'm new using R and CMA. I want to create some classifiers/biomarker from peach microarray data using using the different classification methods implemented in CMA. My problem is that I don't kown how to prepare data and introduce class labels given all examples are based in the prepared dataset golub, but no in a raw gene expression matrix. My goal is to create classifiers based in genotypes and the observed phenotypes. I have a gene expression matrix with 3533 genes (rows) and 48 microarrays corresponding to 16 samples (replicates each). Out of them 8 are from a sensitive and 8 from a tolerant cultivars. Samples are taken at harvest and ripe and two different treatments (3 points each). Please can somebody tell me wich commands I should type to define labels? Thanks a lot in advance Clara
Microarray CMA Microarray CMA • 968 views
ADD COMMENT
0
Entering edit mode
Tim Triche ★ 4.2k
@tim-triche-3561
Last seen 3.5 years ago
United States
This is actually the sort of situation where you might be better off with limma, since the tools for dealing with technical replicates in a nested factorial design (cultivar*resistance) are much better documented in the Limma user's guide. CMA, in my experience, excels at one-way classification problems, but it sounds like you are looking to model which genes change expression according to cultivar, which change according to resistance, and which change as a function of both. Using lmFit() and eBayes() then ranking the top results for each factor might be a more fruitful approach than shoehorning your problem into CMA. But, that's just my opinion, based on my understanding of your experiment. --t On Fri, Jun 24, 2011 at 3:03 AM, Clara Pons <cpons@upvnet.upv.es> wrote: > Hi to all, > I'm new using R and CMA. I want to create some classifiers/biomarker from > peach microarray data using using the different classification methods > implemented in CMA. My problem is that I don't kown how to prepare data and > introduce class labels given all examples are based in the prepared dataset > golub, but no in a raw gene expression matrix. > My goal is to create classifiers based in genotypes and the observed > phenotypes. I have a gene expression matrix with 3533 genes (rows) and 48 > microarrays corresponding to 16 samples (replicates each). Out of them 8 are > from a sensitive and 8 from a tolerant cultivars. Samples are taken at > harvest and ripe and two different treatments (3 points each). > Please can somebody tell me wich commands I should type to define labels? > > Thanks a lot in advance > > Clara > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]
ADD COMMENT

Login before adding your answer.

Traffic: 860 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6