Hi all, QIIME2 studio has for the first time allowed me to start digging into data that was previously the remit of bioinformaticias and statisticians. Many many thanks to the developers. My first question on the forum is on Alpha Diversity Group Significance.
I am currently looking at a dataset (meta analysis) where I believe alpha diveristy may be being impacted by a couple of different meta data fields. Is there a way in Q2 studio to rank the importance of these different meta data fields e.g. age, weight, location to determine an order of importance. Otherwise I will have to run every combination of fields reducing considerable the amount of samples in each set.
Good question! Sounds like bioenv may be what you are looking for. That should narrow down the list of important metadata columns.
Note that alpha-group-significance will automatically run on all categorical metadata columns. alpha-correlation will run on all numeric columns. So you only need to run the commands once and scan on through the results.
Thanks Nick. In my excitement about being able to do this kind of stuff I am running everything I can to be honest!!! The alpha correlation will run on all numeric columns at once which is great. However, from what I can see the alpha group significance has to be run separately for each metadata field of interest. Maybe I should try leaving the metadata field box blank…
I will have a look at bioenv but I thought that was based on beta diversity distances. I guess it could act as an indicator for potential alpha differences but as I am sure you well know, difference in one does not always mean a difference in the other.
Impressed with the speed of reply. Many thanks, I think I shall be keeping a QIIME2 forum open on my desktop from now on!!!