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  • Bio_Red
    Junior Member
    • Mar 2014
    • 2
    #1

    Software to visualize complex DGE data sets?

    I have 45 samples which may or may not cluster according to genotype (three de novos assembled using Trinity), time and/or treatment (T0 control only, T1, control and treatment, T2 control and treatment)

    With so many aspects to consider, can anyone advise how best to analyse and visualize the DGE data I have (processed through EdgeR), and with what software? I had been looking at PCA clustering and Multi-dimensional scaling with web based applications, including VENNT, EXPANDER AND J-Express, but am new to all this and thought it wise to consult first
    Tags: None
  • blancha
    Senior Member
    • May 2013
    • 367
    #2
    I like FactoMineR.
    I'm able to generate very informative PCA plots with it.

    FactoMineR: Exploratory Multivariate Data Analysis with R
    http://factominer.free.fr
    FactoMineR, an R package dedicated to multivariate Exploratory Data Analysis

    Comment

    • Bio_Red
      Junior Member
      • Mar 2014
      • 2
      #3
      Thank you Blancha

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