In order to define ratios between different molecular species within and ultimately between different mass spectra, we performed a normalization step so as to set the median intensities of all the peaks detected within one spectrum to one.
To control this variation, we included a normalization step using genes without APA, as described in detail in Figure S1.
Reverse transcription and amplification of cDNA was done as described by Cheung and coworkers [59] and included a normalization step, which effectively decreased over- expressed reads.
RMA, as introduced by Irizarry et al. [ 8], includes a normalization step, a background adjustment step, and a summarization step.
This encoding ensures zero-means, which obviates a normalization step.
As a further normalization step for ease of comparison between experiments, the vector of expression measures of a given gene in a given strain background and replicate set was centered with respect to the median across the set.
As a pre-processing, normalization step, several elementary transforms are applied to the body at each frame of its trajectory before the computation of descriptors.
As the normalization step shown in equation A induces upper and lower limits of 0 to 1 for the range of φ values, confidence intervals used to define the clusters in each group have the same natural limits.
