Hi all, I performed a gneiss regression analysis on 10 samples with qiime gneiss ols-regression. Weirdly, the model_mse comes out as zeros, where as there are pred_mse values (see screenshot). The regression coefficients summary plot is empty. I would like to check for "over-fitting" and wanted to …

That is interesting. Is the MSE is zero, I'd suspect that overfitting is occurring. An R^2 of 0.91 is also incredibly high for an ols regression. A couple of comments. What do the PCoA plots look like? The R^2 should be comparable to the total variation explained in the top 3 axes (since it is…

Thanks for the comments @mortonjt . What PCoA plots do you mean? Bray Curtis, jaccard, weighted/unweighted unifrac? I am also guessing you suggest to check the bar plot on the right side of the emperor plots (under axes), is that right? I can already tell you that I do have a high fraction of low a…

Pick your favorite abundance based distance. Bray-Curtis/Weighted Unifrac should do. Here, you only have 10 samples. So you probably can only run a regression with a single covariate (you shouldn't fit more covariates than 10% of your samples). I think this is where the overfitting is coming fro…

I see. Does that mean in order to use 1 covariate, the parameter --p-formula would only contain one metric? Such as pH...

@mortonjt I think I got it now. [53 AM] I have a couple of follow up questions though: The red_mse value of the fold_9 row is 0.0000, why is that? Unfortunately the regression coefficients summary plot is still empty: [59 AM] Lastly, what type of plot is below this empty one, showing the pre…

Interesting. This looks more like what I'd expect for linear regression (even though these are extremely small sample sizes). Are you able to download the coefficients, residuals and pvalues on the main simplical linear regression summary? I'm entirely sure what is going on with the coefficient h…

Thanks @mortonjt I just sent you the data for checking.

Hi @steff1088 your pvalues look sane. Are you able to zoom in the coefficient heatmaps? We have noticed that the heatmap appears to be empty sometimes, but will look more sane once you start navigating the heatmap.

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Gneiss balances: Zero values for model mse

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