METASTATS (Help!!)

I am analyzing sanger data (yes, sorry!!! but I have old data and have to work with them!!) and have 8 libraries of 96 clones each. I have to groups, soil (6 libraries) and sediment (2 libraries) communities. I ran metastats with my shared file, obtained from phylotype approach at level=1 and the design file:
M1 SO
M2 SO
M8 SO
M24 SO
M28 SO
M35 SO
M40 SE
M57 SE

The problem is that I get only q values of 1.0000 and I know for the rank plots and the otu abundances that there are some otus that really make difference between the two groups (like OTU1 for the start) and I don’t understand what am I doing wrong?? :?: :?

I want to have some statistics supporting what comes out at plain sight from my data, and I thought this test will be really good for that. Someone can help me understand what is happening please?? I copy the output file below.

Thanks a lot!!!

Local time and date of test: Fri Jul 11 16:46:17 2014

rows = 152, # col = 8, g = 6

1000 permutations

OTU mean(group1) variance(group1) stderr(group1) mean(group2) variance(group2) stderr(group2) p-value q-value
Otu001 0.085069 0.022067 0.060645 0.000000 0.000000 0.000000 0.246943 1.000000
Otu002 0.071181 0.002188 0.019097 0.000000 0.000000 0.000000 0.023132 1.000000
Otu003 0.055556 0.002025 0.018373 0.020833 0.000868 0.020833 0.306774 1.000000
Otu004 0.024306 0.000246 0.006402 0.062500 0.003472 0.041667 0.605755 1.000000
Otu005 0.013889 0.000203 0.005810 0.088542 0.002658 0.036458 0.090283 1.000000
Otu006 0.041667 0.001476 0.015683 0.000000 0.000000 0.000000 0.053943 1.000000
Otu007 0.001736 0.000018 0.001736 0.104167 0.000868 0.020833 0.007717 1.000000
Otu008 0.032986 0.000756 0.011224 0.005208 0.000054 0.005208 0.076358 1.000000
Otu009 0.031250 0.000694 0.010758 0.000000 0.000000 0.000000 0.030755 1.000000
Otu010 0.031250 0.000738 0.011089 0.000000 0.000000 0.000000 0.036717 1.000000
Otu011 0.029514 0.000669 0.010560 0.000000 0.000000 0.000000 0.038151 1.000000
Otu012 0.029514 0.000626 0.010212 0.000000 0.000000 0.000000 0.034396 1.000000
Otu013 0.005208 0.000076 0.003558 0.062500 0.000868 0.020833 0.049340 1.000000
Otu014 0.012153 0.000235 0.006260 0.041667 0.000217 0.010417 0.066396 1.000000
Otu015 0.013889 0.000289 0.006944 0.020833 0.000868 0.020833 0.878792 1.000000
Otu016 0.001736 0.000018 0.001736 0.052083 0.000217 0.010417 0.010302 1.000000
Otu017 0.019097 0.000582 0.009852 0.000000 0.000000 0.000000 0.101623 1.000000
Otu018 0.000000 0.000000 0.000000 0.057292 0.000054 0.005208 0.002849 0.813019
Otu019 0.015625 0.000076 0.003558 0.010417 0.000217 0.010417 0.797302 1.000000
Otu020 0.017361 0.000333 0.007447 0.000000 0.000000 0.000000 0.074623 1.000000
Otu021 0.017361 0.000289 0.006944 0.000000 0.000000 0.000000 0.057755 1.000000
Otu022 0.015625 0.000423 0.008398 0.000000 0.000000 0.000000 0.118245 1.000000
Otu023 0.013889 0.000246 0.006402 0.005208 0.000054 0.005208 0.363208 1.000000
Otu024 0.015625 0.000163 0.005208 0.000000 0.000000 0.000000 0.027604 1.000000
Otu025 0.012153 0.000235 0.006260 0.005208 0.000054 0.005208 0.628075 1.000000
Otu026 0.013889 0.000637 0.010300 0.000000 0.000000 0.000000 0.262660 1.000000
Otu027 0.010417 0.000651 0.010417 0.010417 0.000000 0.000000 0.990000 1.000000
Otu028 0.010417 0.000087 0.003804 0.005208 0.000054 0.005208 0.659547 1.000000
Otu029 0.012153 0.000148 0.004971 0.000000 0.000000 0.000000 0.062094 1.000000
Otu030 0.000000 0.000000 0.000000 0.031250 0.001953 0.031250 0.370830 1.000000
Otu031 0.006944 0.000029 0.002196 0.010417 0.000217 0.010417 0.867057 1.000000
Otu032 0.010417 0.000260 0.006588 0.000000 0.000000 0.000000 0.159264 1.000000
Otu033 0.010417 0.000651 0.010417 0.000000 0.000000 0.000000 0.370830 1.000000
Otu034 0.000000 0.000000 0.000000 0.031250 0.000217 0.010417 0.027604 1.000000
Otu035 0.001736 0.000018 0.001736 0.026042 0.000488 0.015625 0.193075 1.000000
Otu036 0.000000 0.000000 0.000000 0.031250 0.000868 0.020833 0.207396 1.000000
Otu037 0.010417 0.000043 0.002690 0.000000 0.000000 0.000000 0.015000 1.000000
Otu038 0.008681 0.000148 0.004971 0.000000 0.000000 0.000000 0.339099 1.000000
Otu039 0.000000 0.000000 0.000000 0.026042 0.000488 0.015625 0.146623 1.000000
Otu040 0.005208 0.000163 0.005208 0.010417 0.000217 0.010417 0.809075 1.000000
Otu041 0.008681 0.000061 0.003201 0.000000 0.000000 0.000000 0.339099 1.000000
Otu042 0.008681 0.000452 0.008681 0.000000 0.000000 0.000000 0.339099 1.000000
Otu043 0.008681 0.000061 0.003201 0.000000 0.000000 0.000000 0.339099 1.000000
Otu044 0.005208 0.000033 0.002329 0.010417 0.000217 0.010417 0.791887 1.000000
Otu045 0.000000 0.000000 0.000000 0.026042 0.000488 0.015625 0.146623 1.000000
Otu046 0.006944 0.000072 0.003472 0.000000 0.000000 0.000000 0.577023 1.000000
Otu047 0.006944 0.000072 0.003472 0.000000 0.000000 0.000000 0.577023 1.000000
Otu048 0.006944 0.000072 0.003472 0.000000 0.000000 0.000000 0.577023 1.000000
Otu049 0.006944 0.000072 0.003472 0.000000 0.000000 0.000000 0.577023 1.000000
Otu050 0.006944 0.000116 0.004392 0.000000 0.000000 0.000000 0.577023 1.000000
Otu051 0.006944 0.000289 0.006944 0.000000 0.000000 0.000000 0.577023 1.000000
Otu052 0.006944 0.000289 0.006944 0.000000 0.000000 0.000000 0.577023 1.000000
Otu053 0.006944 0.000289 0.006944 0.000000 0.000000 0.000000 0.577023 1.000000
Otu054 0.000000 0.000000 0.000000 0.020833 0.000000 0.000000 0.000000 0.000000
Otu055 0.000000 0.000000 0.000000 0.015625 0.000488 0.015625 0.370830 1.000000
Otu056 0.003472 0.000072 0.003472 0.005208 0.000054 0.005208 1.000000 1.000000
Otu057 0.000000 0.000000 0.000000 0.015625 0.000054 0.005208 0.027604 1.000000
Otu058 0.005208 0.000033 0.002329 0.000000 0.000000 0.000000 0.577207 1.000000
Otu059 0.005208 0.000076 0.003558 0.000000 0.000000 0.000000 0.577207 1.000000
Otu060 0.005208 0.000076 0.003558 0.000000 0.000000 0.000000 0.577207 1.000000
Otu061 0.005208 0.000076 0.003558 0.000000 0.000000 0.000000 0.577207 1.000000
Otu062 0.005208 0.000076 0.003558 0.000000 0.000000 0.000000 0.577207 1.000000
Otu063 0.005208 0.000076 0.003558 0.000000 0.000000 0.000000 0.577207 1.000000
Otu064 0.005208 0.000076 0.003558 0.000000 0.000000 0.000000 0.577207 1.000000
Otu065 0.005208 0.000076 0.003558 0.000000 0.000000 0.000000 0.577207 1.000000
Otu066 0.000000 0.000000 0.000000 0.015625 0.000488 0.015625 0.370830 1.000000
Otu067 0.005208 0.000033 0.002329 0.000000 0.000000 0.000000 0.577207 1.000000
Otu068 0.005208 0.000076 0.003558 0.000000 0.000000 0.000000 0.577207 1.000000
Otu069 0.005208 0.000163 0.005208 0.000000 0.000000 0.000000 0.577207 1.000000
Otu070 0.005208 0.000076 0.003558 0.000000 0.000000 0.000000 0.577207 1.000000
Otu071 0.005208 0.000033 0.002329 0.000000 0.000000 0.000000 0.577207 1.000000
Otu072 0.005208 0.000033 0.002329 0.000000 0.000000 0.000000 0.577207 1.000000
Otu073 0.001736 0.000018 0.001736 0.010417 0.000217 0.010417 0.645434 1.000000
Otu074 0.000000 0.000000 0.000000 0.010417 0.000217 0.010417 0.370830 1.000000
Otu075 0.003472 0.000072 0.003472 0.000000 0.000000 0.000000 1.000000 1.000000
Otu076 0.003472 0.000029 0.002196 0.000000 0.000000 0.000000 1.000000 1.000000
Otu077 0.001736 0.000018 0.001736 0.005208 0.000054 0.005208 0.437744 1.000000
Otu078 0.003472 0.000029 0.002196 0.000000 0.000000 0.000000 1.000000 1.000000
Otu079 0.000000 0.000000 0.000000 0.010417 0.000217 0.010417 0.370830 1.000000
Otu080 0.000000 0.000000 0.000000 0.010417 0.000217 0.010417 0.370830 1.000000
Otu081 0.000000 0.000000 0.000000 0.010417 0.000217 0.010417 0.370830 1.000000
Otu082 0.003472 0.000029 0.002196 0.000000 0.000000 0.000000 1.000000 1.000000
Otu083 0.003472 0.000029 0.002196 0.000000 0.000000 0.000000 1.000000 1.000000
Otu084 0.003472 0.000072 0.003472 0.000000 0.000000 0.000000 1.000000 1.000000
Otu085 0.003472 0.000072 0.003472 0.000000 0.000000 0.000000 1.000000 1.000000
Otu086 0.003472 0.000029 0.002196 0.000000 0.000000 0.000000 1.000000 1.000000
Otu087 0.000000 0.000000 0.000000 0.010417 0.000217 0.010417 0.370830 1.000000
Otu088 0.003472 0.000072 0.003472 0.000000 0.000000 0.000000 1.000000 1.000000
Otu089 0.003472 0.000029 0.002196 0.000000 0.000000 0.000000 1.000000 1.000000
Otu090 0.003472 0.000072 0.003472 0.000000 0.000000 0.000000 1.000000 1.000000
Otu091 0.003472 0.000072 0.003472 0.000000 0.000000 0.000000 1.000000 1.000000
Otu092 0.003472 0.000029 0.002196 0.000000 0.000000 0.000000 1.000000 1.000000
Otu093 0.003472 0.000072 0.003472 0.000000 0.000000 0.000000 1.000000 1.000000
Otu094 0.001736 0.000018 0.001736 0.005208 0.000054 0.005208 0.437744 1.000000
Otu095 0.003472 0.000072 0.003472 0.000000 0.000000 0.000000 1.000000 1.000000
Otu096 0.003472 0.000029 0.002196 0.000000 0.000000 0.000000 1.000000 1.000000
Otu097 0.000000 0.000000 0.000000 0.010417 0.000217 0.010417 0.370830 1.000000
Otu098 0.003472 0.000072 0.003472 0.000000 0.000000 0.000000 1.000000 1.000000
Otu099 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu100 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu101 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu102 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu103 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu104 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu105 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu106 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu107 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu108 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu109 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu110 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu111 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu112 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu113 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu114 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu115 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu116 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu117 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu118 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu119 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu120 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu121 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu122 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu123 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu124 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu125 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu126 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu127 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu128 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu129 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu130 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu131 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu132 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu133 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu134 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu135 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu136 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu137 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu138 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu139 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu140 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu141 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu142 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu143 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu144 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu145 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu146 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu147 0.000000 0.000000 0.000000 0.005208 0.000054 0.005208 0.250000 1.000000
Otu148 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu149 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu150 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu151 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000
Otu152 0.001736 0.000018 0.001736 0.000000 0.000000 0.000000 1.000000 1.000000

I think part of the problem might be that you have six samples in one group and two samples in the second group. Because this is a non-parametric test, you are kind of limited to how small of p-values you can obtain. This is a permutation-based test so there’s only so many way to assign 8 samples to 2 groups when one of them only has 2 samples.

Pat

Thank you Pat!!! It seems that I cannot find a test to support statistically what I see at plain sight from my results. I wanted to support the fact that some populations are really making a difference between the impacted and control samples. I’ll have to go only with bar plots of abundances as not even ordination is supported by the stress and R2, although the separation of the samples looks logical. Is there any test to compare let’s say two samples? or small groups of samples?