Aldex2 error when processing picrust2 output

[Nicholas_Bokulich]

Hi @didietkeren,
I have moved this topic to "community plugin support" because it concerns q2-picrust2 and q2-aldex2, both of which are community plugins.

The error message is quite clear:

@didietkeren

Error in aldex.clr.function(as.data.frame(reads), conds, mc.samples, denom, :
not all reads are integers

aldex2 is looking for integer counts, but picrust2 can output non-integer values as described here:

why PICRUSt2 ko_metagenome prediction generates non-integer result?

Hi @Lennon_Lee, The output predicted abundances are the result of multiplying the normalized # of 16S reads for each ASV by the number of KO copies per predicted genome for that ASV. The output is non-integers because the the normalized 16S read counts are generated by dividing the raw 16S abundances by the predicted number of 16S copies in that ASV's genome. I think it's reasonable to round the counts if you want to use DEseq2. I would be more worried about which model to use with DEseq2 bec…

This is why an ASV table works (all values are integers) but picrust2 output does not. Looks like you will need to round those results somehow before passing to aldex2.

Good luck!

cc: @dgiguer and @gmdouglas in case you have anything to add.