Hi, i ran get.microbiome and it sounds useful but i am having trouble understanding the output file. I have 28 samples and the left column states my samples from 1 to 28 . However, i can’t figure which group is samples 1? my groups are numbered G1 to G28. Anyhelp would be great .
You mean get.coremicrobiome?
The first column indicates the number of samples that the OTUs are found in. From the wiki page:
The entries in the table represents the fraction of OTUs in a study that have a relative abundance at or above %X in at least %Y samples. X goes from 0 to 100, Y from 1 to the number of samples in your dataset. From the above file we can see that 0.615385 (roughly 62%) of the OTUs have a relative abundance at or above 0.01 in at least one sample, but only 0.230769 (roughly 23%) have a relative abundance at or above 0.01 in all the samples.
thanks Pat, the first column indicates the numbers of the samples but can these samples be defined i.e. when it says 5, 6, etc samples , can we determine those samples?
That’s in the shared file. This command aggregates the data to see the % of OTUs that show up in N OTUs X% of the time.