mixMC normalization for microbiome RNA-seq data

Analysis
#1

Dear all,

I am wondering if the same normalization described for 16S microbiome studies described in the mixMC paper can be applied for microbiome count data coming from a RNA-seq study.
In my case, I mapped the RNA-seq reads using the Centrifuge/Recentrifuge pipeline.

Thanks,

#2

hi @aec,
there are many normalisation methods for RNA-seq. Even if they disregard the compositionality issue, I would favour them. That said, there is no counter indication to use the approach proposed in mixMC (see the updated steps here: http://mixomics.org/mixmc/mixmc-pre-processing/), especially if your data are sparse.

Kim-Anh

#3

Thanks Kim Anh. I was not sure that the normalizations used by edgeR or DESeq2 for differential gene expression could be applied for microbiome studies using RNA-seq. My problem is that the number of reads that are classified as microbial species is extremely variable across my human samples and I was looking for an alternative to rarefraction.