Hello all,
This is my first time analysing NGS (16s) data and I’m following the Miseq SOP. I’m trying to use the HOMOVA command to compare variation between 4 microbial communities. It has worked twice perfectly, for example:
homova(phylip=stability.an.thetayc.0.03.lt.ave.dist, design=14design7.design)
Output:
HOMOVA BValue P-value SSwithin/(Ni-1)_values
1-14-2-8 2.11872 0.004* 0.255805 0.0589287 0.12989 0.155421
1-14 2.08415 0.004* 0.255805 0.0589287
1-2 0.326683 0.198 0.255805 0.12989
1-8 0.218445 0.214 0.255805 0.155421
14-2 0.537003 0.115 0.0589287 0.12989
14-8 0.936382 0.012 0.0589287 0.155421
2-8 0.023833 0.657 0.12989 0.155421
However, when attempting to use HOMOVA on a different set of 4 communities I don’t get the same output - the pairwise comparisons have disappeared:
mothur > homova(phylip=stability.an.thetayc.0.03.lt.ave.dist, design=14design0.design)
Output:
HOMOVA BValue P-value SSwithin/(Ni-1)_values
A-D-B-C 0.315196 0.281 0.203007 0.134267 0.218678 0.121459
These are the two design files for comparison:
14design7.design
group box
R1.1 1
R1.2 1
R1.3 1
R1.4 1
R1.5 1
R1.6 1
R2.1 2
R2.2 2
R2.3 2
R2.4 2
R8.1 8
R8.2 8
R8.3 8
R8.4 8
R8.5 8
R14.1 14
R14.2 14
R14.3 14
R14.4 14
R14.5 14
R14.6 14
14design0.design
group box
A.1 A
A.2 A
A.3 A
A.4 A
A.5 A
A.6 A
B.1 B
B.2 B
B.3 B
C.1 C
C.2 C
C.3 C
D.1 D
D.2 D
D.3 D
D.4 D
D.5 D
D.6 D
But I don’t think the 14design0.design file is at fault because the two design files are nearly identical and i get the pairwise comparisons in the AMOVA ouptut using that design file.
Any ideas or suggestions as to why this is happening and what I could do to fix this? Thanks!