I just followed the tutorial that provided by mixOmics team and I am still confusing about two issues.
In Pre-processing OTU table(I use ASV-table generated by DADA2,but I think it is the same type) section, the tutorial use TSS (relative abundance) as the normalisation method.
Generally " Rarefy"(Subsamples an OTU table to a fixed number of reads per sample using random subsampling without replacement") has been recommanded both Usearchv11 and QIIME2.
Usearch author Robert Edgar even said it is the best strategy for microbiome dataset since it preserves the shape of the abundance distribution in each sample more accurately than systematic rounding as used in the obsolete otutab_norm(CSS method) command.
So I want to know if Rarefy method can be used as processing method for mixMC.
And if yes how do I deal with the rarefied OTU/ASV table next? Should I follow another TSS normalisation? Or other log ratio transformation?
I want to intergrating my microbiome data with a metabolomics data which contains the volatile organic compound（voc）and organic acid(oa) concentrations in sample,which is measured by GC-MS. I think I should use PLS/sPLS ,am I right?
Also the voc and oa concentrations have already calculated and conversed to the same unit（such as mg/g）,do I still need to normalised it?
Hope somebody can give me some advice! Thank you!