I have two questions:

QUESTION 1. In metagenomeSeq:

# Calculate proper percentile to normalize data

percentile = cumNormStatFast(genusObj, pFlag = FALSE, rel = 0.1)

percentile

genusObj = cumNorm(genusObj, p = percentile)

genusObj

If I substitute p = percentile by p = 1 , will metagenomeSeq perform total sum normalization? 

QUESTION 2:

Is it possible to conduct DESeq and TMM normalization using metagenomeSeq?

Many thanks in advance!

Hi Jovel, Thanks for the interest. First, an answer to your first question: Yes, setting the p = 1 will result in total sum normalization.

To answer the second question: Yes, it is possible to use any other scaling method, please see: A: normFactors when aggregating in metagenomeSeq 

pData(obj@expSummary$expSummary)$normFactors = values

Thanks for the prompt response. It was really helpful!