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ggloor / ALDEx2_dev

ALDEx tool to examine compositional high-throughput sequence data with Welch's t-test
GNU Affero General Public License v3.0
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Interpreting ALDEx2 results #9

Closed nearinj closed 5 years ago

nearinj commented 5 years ago

Hello,

I have been using ALDEx2 extensively to find differential features (taxa) between case and control saliva microbiome samples. Using a q-value cutoff of 0.05 I have found some puzzling results where the distributions and median values of features are similar but are still called differential abundant. An example of this can be seen from this boxplot:

ALDEX results:

effect: 0.2778, wi.eBH=0.0168

Aldex_results

Similar plots are also found for other features that were called. I'm trying to figure out why these features are being called differential abundant when it looks like they have very similar relative abundances (as shown by the boxplot). Is this due to my experimental design having a large class imbalance 1:5 (case:control) or perhaps I need to also implement an effect size cutoff as well (which is hard to estimate what a "good" cutoff would be).

nearinj commented 5 years ago

After further thought I realised that it may be better to visualise the results as CLR values (rather than RA)... this seems to have fixed up the plots a bit and perhaps solved the issue.

clr_github_issue png

Thanks Jacob Nearing