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  • SylvainL
    Senior Member
    • Feb 2012
    • 180
    #1

    Number of clusters for Timecourse

    Hi, I have to analyze RNAseq time-course (4 timepoints, each in triplicates) and I would like to calculate the number of clusters...

    I had a look at this page
    Cluster analysis in R: determine the optimal number of clusters
    http://stackoverflow.com/questions/15376075/cluster-analysis-in-r-determine-the-optimal-number-of-clusters
    How can I choose the best number of clusters to do a k-means analysis. After plotting a subset of below data, how many clusters will be appropriate? How can I perform cluster dendro analysis? n = 1...


    which gives a lot of explanations but I hesitate about the proper way to go...

    I was thinking about using RPKM values (for all the samples, i-e 12 different values for each genes), and I still wonder if the resulting matrix would be appropriated as input (replacing matrix d in the examples).

    Can anyone help me?

    Thanks in advance,

    s.
    Tags: None
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