Thom Quinn

Hi Meggy, There are a few options here. Given that your data are already CLR transformed, you can fit a glm model directly, as you would for any other data....

Note that the GLM will test each OTU one at a time, via the formula `OTU_i ~ Covariates`. If you want to perform a fully multivariable analysis, you could instead...

Hey SilasK, thanks for your interest in propr! Regarding dimensional reduction in CoDa, I would tend to run a CLR (or some variant) on the _sample rows_, then perform a...

Regarding "I tried the CLR-PCA and found that the dominating 1 PC is strongly correlated with the number of counts. I hoped that the CoDa based method would remove (at...

G'day, and thanks for your interest in propr. Are you suggesting that that you have multiple data sets which come from the same samples? For example, 16s data, pathway data,...

Ah yes! Now we're on the same page! > Had though that CoDa would operate well between multiomics sets, assuming each set had an appropriately chosen denominator. This is correct....

If you perform your own (multi-omic) transformation, you can now pass it through propr, and access all of the helper/wrapper functions. Here is a reproducible example for you. ``` devtools::install_github("tpq/propr")...

Hi Jemma, thanks for your interest in `propr`. For a data set where rows are samples and columns are features, the CLR should be performed row-wise. So in your case...

Yes, that'd be it!

Hey Taylor! Thanks for your interest in propr, and for asking such detailed questions! I'll try to answer them quickly now, but I also invite follow-up questions. (1) > Is...