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The percentile rankings of real data from the normalized PLV values within the surrogate distributions were used to assess the statistical significance of observed changes in synchronization.
The average probe intensity (average of antilogs of the raw data) from the normalized data for all replicates of each parasite isolate was calculated.
The neqc function of the limma [ 62] package was used to perform a normal-exponential convolution model analysis to estimate non-negative signal, quantile normalization using all probes (gene and control, detected and not detected) and samples, addition of a recommended (small) offset, log2 transformation, and elimination of control probe data from the normalized expression matrix.
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Since microarray data analysis can be affected by a number of bias [40], we put a particular care on study design and analysed data from the 48 normalized microarrays using multi-way analysis of variance (ANOVA) [41].
Expression data from the microarray was normalized using polynomial fitting.
(B ) Run-length data from (A ), normalized to the baseline run length value for each construct.
5 Data from the microarray analysis were normalized for dye and microarray effects (ie, Lowess normalization and array centering) and used for statistical analysis.
The normalized data from the literature show that the cells/biomass and PHB kinetics (Additional file 1: Figures S1 and S2) always have the same behavior and that they are independent to: culture systems, operating conditions, culture media, bioreactors used or the techniques used to measure.
For the NL interaction profile after SU HW) knockdown, the normalized data from the different dsRNA amplicons were averaged as well.
We downloaded the normalized data from the GEO database.
The normalized data from the experiments were fit into linear models using the Bioconductor package limma[ 15].
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