I am having trouble with composing a dataset made by 3 different runs, but in particular with 2 different library preparations, which to my knowledge, based on RNASeq experience, is the major cause of batch.
I have just run my microbiome pipeline starting from fastqs, however when I go for alfa diversity I can appreciate the effect of the two library preparations. In addition to that if I run the wilcoxon. test on alfa- diversity I see a significant result.
The same appears when I run beta diversity and adonis test on this category (different sequencing library preparation).
I imagined to use abundance values and correct the batch in a linear model, however I am not that sure this would be sufficient and in any case the differences I can see in alfa diversity suggest that in one preparation I can count more OTU, while in the other one that is not the case.
Could you give me advice on how to face those situations?
Thanks a lot,