Normalization factors in metagenomeSeq
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jovel_juan ▴ 10
@jovel_juan-7129
Last seen 9 months ago
Canada

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!

 

microbiome • 1.2k views
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@joseph-nathaniel-paulson-6442
Last seen 4.4 years ago
United States

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
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jovel_juan ▴ 10
@jovel_juan-7129
Last seen 9 months ago
Canada

Thanks for the prompt response. It was really helpful!

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