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  • johnsequence
    Member
    • Jan 2010
    • 22
    #1

    affymetrix snp 6

    Hello,

    I am running a set of affymetrix snp 6.0 chip and new in DNA stuff. Could you please recommend some softwares (e.g. R based packages)? Thanks a lot.

    John
    Tags: affymetrix, snp chip 6.0
  • RDW
    Member
    • Oct 2008
    • 63
    #2
    What's your application? For copy number analysis, the free Affymetrix Genotyping Console is pretty nice if you want a GUI tool, or try the Affymetrix Power Tools for command line versions of the algorithms. For LOH I've got better results with dChip. For an R-based framework try aroma.affymetrix. Broad's IGV is good for displaying data from multiple arrays, and their Ultrasome package does very fast copy number segmentation. Links to all these are on the aroma.affymetrix tools page:

    404 Not Found
    http://aroma-project.org/node/80


    I still also use an old and probably unmaintained package called CGH Explorer for looking at individual copy number profiles in detail:

    CGH-Explorer: a program for analysis of array-CGH data - PubMed
    http://www.ncbi.nlm.nih.gov/pubmed/15531610
    CGH-Explorer is a program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of …

    Comment

    • Sam64
      Member
      • Jun 2011
      • 15
      #3
      I use Partek genomic software but the licence is not free
      Sam64

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