Permutation based MANCOVA with stepwise variable selection results for Sanger, 454 V1–V3 and 454 V3–V5 sequencing.

The dependent variable was the vector generated by the centered log ratio of the relative frequencies of six phyla/subphyla categories (see text). The significant main effects and first order interactions selected by analysis of each of the three data sets as well as the R2, P values are listed here. To address multiple comparison issues, the Benjamini-Hochberg method was applied to adjust P-values to the false discovery rate (FDR). The number of samples (total = 170 samples) that yielded results suitable for analysis is listed for each method.