normalising before lefse? (picrust2 to lefse)

[Marwa Tawfik]

Hello 

Could you please share with me your recommended way of normalising before using lefse?

I am using microbiomeMarker (run_lefse function) to do so

A good tutorial is here;

https://www.bioconductor.org/packages/devel/bioc/vignettes/microbiomeMarker/inst/doc/microbiomeMarker-vignette.html

They provide seven popular normalization methods, including:

• rarefy: random subsampling counts to the smallest library size in the data set.
• TSS: total sum scaling, also referred to as “relative abundance”, the abundances were normalized by dividing the corresponding sample library size.
• TMM: trimmed mean of m-values. First, a sample is chosen as reference. The scaling factor is then derived using a weighted trimmed mean over the differences of the log-transformed gene-count
  fold-change between the sample and the reference.
• RLE: relative log expression, RLE uses a pseudo-reference calculated using the geometric mean of the gene-specific abundances over all samples. The scaling factors are then calculated as the median of the gene counts ratios between the samples and the reference.
• CSS: cumulative sum scaling, calculates scaling factors as the cumulative sum of gene abundances up to a data-derived threshold.
• CLR: centered log-ratio normalization.
• CPM: pre-sample normalization of the sum of the values to 1e+06.