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Old 06-26-2015, 03:01 AM   #1
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Location: Germany

Join Date: Sep 2012
Posts: 8
Default PC Axis?

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 at 05:10 AM.
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