...

• Subtract
  When mean, median, Q1, Q3, std dev or sum is selected, the corresponding statistics will be calculated based on the transform on sample or features option
  Example: If transform on Samples is selected, Subtract mean is calculated as:
  TX_sf = X_sf - M_s
  where Ms is the mean of the sample
  Example: If transform on Features is selected, Subtract mean is calculated as:
  TX_sf = X_sf - M_f
  where  M_f is the mean of the feature
• TMM (Trimmed mean of M-values)
  The scaling factors is produced according to the algorithm described in Robinson et al [4]. The paper by Dillies et al. [5] contains evidence that TMM has an edge over other normalization methods. The reference sample is randomly selected. When perform the trimming, for M values (fold change), the upper 30% and lower 30% are removed; for A values (absolute expression), the upper 5% and lower 5% are removed.
  
  
• TPM (Transcripts per million as described in Wagner et al [6])
  The following steps are performed:

...