I have a group that collected fecal samples with the omni-gut kit and gave me duplicates from each sample to process. I ran them through mothur treating each of the duplicates as its own sample. But they really want me to “average” the duplicates.
Would you do that in mothur or R? I can average the alpha diversity pretty easily in R, but am mentally stuck on how to average the lower triangle dist matrices. I’ve been thinking about converting from lt to 3 column dist, replace the sample name with replicate a or b with just sample name, then concat col1 and col2, average, split col1 and col2 apart again, then turn back into lt matrix. But that seems to be a not smart way to approach this.