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- 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:
TXsf = Xsf - Ms
where Ms is the mean of the sample
Example: If transform on Features is selected, Subtract mean is calculated as:
TXsf = Xsf - Mf
where Mf 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:
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