Multiple corrections and unique sequences

Theory behind mothur
1

Hello,

I have been using mothur for many years now, and have always used Metastats to assess shifts in relative abundance using the outputted q-values. I have a couple of questions:

Firstly, in the more recent versions of mothur, the q-values are no longer outputted. Out of curiosity - why is this the case?

Secondly, in the age of analysing unique sequences, how can multiple corrections be applied and justified? It gets to the point where highly significant P-values have a q-value of 1, due to the sheer number of comparisons (in my case, over 10000 OTUs). I wonder whether focussing on the core microbiome is a good solution?

Many thanks,

Jo

2

Hi Jo,

The q-values were pretty screwy and we decided to leave it to you all to pick your preferred way of correcting p-values.

I would screen my OTUs before running the test. Basically, I’d only look at OTUs that are in some minimum number of samples or that have some minimum relative abundance across all of the samples.

Hope this helps a bit…
Pat

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