[BioC] Best options for cross validation machine learning

[Lavinia Gordon]

     Message: 9
     Date: Tue, 19 Jan 2010 16:11:14 +0000
     From: Daniel Brewer <daniel.brewer at icr.ac.uk>
     To: Bioconductor mailing list <bioconductor at stat.math.ethz.ch>
     Subject: [BioC] Best options for cross validation machine learning
     Content-Type: text/plain; charset=ISO-8859-1

   Hi Dan,

     Hello,
     I have a microarray dataset which I have performed an unsupervised
     Bayesian clustering algorithm on which divides the samples into four
     groups.  What I would like to do is:
     1) Pick a group of genes that best predict which group a sample belongs
     to.
     2) Determine how stable these prediction sets are through some sort of
     cross-validation (I would prefer not to divide my set into a training
     and test set for stage one)
     These steps fall into the supervised machine learning realm which I am
     not familiar with and googling around the options seem endless.  I was
     wondering whether anyone could suggest reasonable well-established
     algorithms to use for both steps.

   Have a look at:
   [1]http://cran.ms.unimelb.edu.au/web/views/MachineLearning.html
   I would suggest going through the literature and looking at some papers that
   have dealt with your type of data as some of these packages are really aimed
   at specific types of data, e.g. tumor classification, survival data.
   E.g  see [2]http://www.pnas.org/content/98/19/10869.[3]abstract
   
     Many thanks
     Dan
     --
     **************************************************************
     Daniel Brewer, Ph.D.
     Institute of Cancer Research
     Molecular Carcinogenesis
     Email: daniel.brewer at icr.ac.uk
     **************************************************************
     The Institute of Cancer Research: Royal Cancer Hospital, a charitable
     Company Limited by Guarantee, Registered in England under Company No.
     534147 with its Registered Office at 123 Old Brompton Road, London SW7
     3RP.

   Lavinia Gordon
   Research Officer
   Bioinformatics
   Murdoch Childrens Research Institute
   Royal Children's Hospital
   Flemington Road Parkville Victoria 3052 Australia
   telephone: +61 3 8341 6221
   [4]www.mcri.edu.au
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References

   1. http://cran.ms.unimelb.edu.au/web/views/MachineLearning.html
   2. http://www.pnas.org/content/98/19/10869.abstract
   3. http://www.pnas.org/content/98/19/10869.abstract
   4. http://www.mcri.edu.au/