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  • PCoA

    Dear All,

    I have 16s data and have some queries regarding the same.
    I am doing PCoA analysis and Axis 1 and 2 are not showing a separation of sample based on specific factor, so i plotted to axis 3 and 4 which shows sample separation.
    My question is it unfair to choose axis other than 1 and 2 which generally show maximum variance.
    I always assumed that Statistical test will tell you the significant differences and then you can plot any 2 axis which shows the separation of significant factors.
    Sometimes first two axis are not always the correct axis showing the variance for the factor which are found significant p value.
    And that's the reason i changed the axis.
    Please provide me a valuable suggestion to undo my dilemma
    Also if someone have a scientific journal where they too have used other that first and second axis.
    Thank you looking forward for the reply!!
    Last edited by naman; 10-01-2015, 04:10 AM.

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