Not getting pairwise comparisons AMOVA

Commands in mothur
1

Hi,

I have a matrix of 577 rows/columns which represent samples from different months, a whole year… below is samples for two groups in January.
I run the AMOVA, but I don’t get any pairwise comparisons between month, just one comparison for all months (as seen below). How is that? I have run similar data containing, e.g. 6 different treatments and gotten pairwise comparisons…

  • 1Ao10 Jan
    1Ao11 Jan
    1Ao12 Jan
    1Ao13 Jan
    1Ao14 Jan
    1Ao15 Jan
    1Ao16 Jan
    1Ao17 Jan
    1Cr30 Jan
    1Cr31 Jan
    1Cr32 Jan
    1Cr33 Jan
    1Cr34 Jan
    1Cr35 Jan
    1Cr36 Jan
    1Cr37 Jan
    1Cr38 Jan
    1Cr39 Jan
Apr-Aug-Dec-Feb-Jan-Jul-Jun-Mar-May-Nov-Oct-Sep 
        Among Within Total
SS 0.0541001 13.7769 13.831
df 11 565 576
MS 0.00491819 0.024384

Fs: 0.201698
p-value: 1

Thanks

2

Mothur only calculates the pairwise comparisons if the p-value <= Experiment-wise error rate. In version 1.28.0 you can select sets and force the pairwise comparison if you would like.

mothur > amova(phylip=yourPhylipFile, design=yourDesignFile, sets=Jan-Feb)

would result in the pairwise comparison of Jan and Feb.

3

I have a matrix of 577 rows/columns which represent samples from different months, a whole year… below is samples for two groups in January.
I run the AMOVA, but I don’t get any pairwise comparisons between month, just one comparison for all months (as seen below). How is that?

Well, we’re protecting you from yourself :). If there is not a significant effect at the experiment level, there won’t be one at the group by group level.

4

Ok, thanks! :slight_smile: