Total counts |
Calculates scaling factors based on the total gene abundances |
- |
Median |
Calculates scaling factors based on the median gene abundance |
edgeR package in Bioconductor |
Upper quartile [19] |
Calculates scaling factors based on the upper quartile of the gene abundances |
edgeR package in Bioconductor |
Trimmed mean of M-values (TMM) [21] |
Calculates scaling factors based on robust analysis of the difference in relative abundance between samples. |
edgeR package in Bioconductor |
Relative Log Expression (RLE) [30] |
Calculates scaling factors using the ratio between gene abundances and their geometric mean |
DESeq package in Bioconductor |
Cumulative sum scaling (CSS) [20] |
Calculates scaling factors as the cumulative sum of gene abundances up to a data-derived threshold |
metagenomeSeq package in Bioconductor |
Reversed cumulative sum scaling (RCSS) |
Calculates scaling factors as the cumulative sum of high abundant genes |
- |
Quantile-quantile [19] |
Transforms each sample to follow a data-derived reference distribution |
- |
Rarefying [55] |
Randomly removes gene fragments until the sequencing depth is equal in all samples |
phyloseq package in Bioconductor |