I tried to obtain the taxonomy relative abundance, using the commands suggested in Processing Questions (visualizations and taxonomy assignment) (anyway, I will report the commands below).
I got this table (level-2-relativa.qzv) and I don’t understand the results, especially in the frequency column (in the picture below). Maybe, I missed something in the command.
Looks like this is our bad. Our visualization seems to kind of assume it’s dealing with counts everywhere, but it’s type definitely accepts RelativeFrequency and PresenceAbsence.
In the meanwhile, you can download the .csv file at the bottom of the first tab in your visualization. However, these are the summed per-sample proportions which don’t have a super intuitive interpretation (and you are going to be fighting floating-point rounding errors).
What questions are you trying to answer with this data?
I downloaded the file.csv, anyway my doubt was: for example, if I consider sample of “Bacteria_Proteobacteria; Frequency 22; # of Sample Observed In 25”, is 22 Frequency value the relative abundance of Proteobacteria? If not, what is it?
May you please explain to me what do you mean with “it’s type definitely accepts RelativeFrequency and PresenceAbsence”?
However, the visualization itself is probably better suited to only showing
FeatureTable[Frequency]
which would have prevented you from passing a
FeatureTable[RelativeFrequency]
and getting that relatively nonsense feature-sum of 22.891869805385593.
What is your current goal with looking at the level-2 taxonomy abundance? There's probably a better way to get that information (usually qiime taxa barplot).
Thank you @ebolyen For your answer!!
I already did the QIIME taxa barplot, but the output is absolute abundances. My aim is to transform the absolute abundance table in relative abundance table, without doing it by my self in excel.
Do you know another way to do relative abundance table output?
Good news is you have already succeeded in that effort! It is just your table summary that is nonsensical. If you export Level-2-relativa.qza you will find a relative abundance .biom table which you can convert as needed via biom convert.
