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After data processing each probe was tested over replicates for changes in expression between different conditions using an empirical Bayes moderated t statistic, i.e. Limma [ 37] and/or Rank Products [ 38].
After data processing as indicated in [ 17], each probe was tested over replicates for changes in expression between different conditions using an empirical Bayes moderated t statistic, i.e. Limma [ 18].
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Non-instructed subjects were required to discriminate between the different conditions using their own-developed manipulation technique during a familiarization phase.
The dispensed volume was weighed and an ordinary one-way ANOVA was used (GraphPad Prism version 7.00 for Mac, GraphPad Software, La Jolla California USA) to estimate the statistical difference between the different conditions used in Supplementary Fig. 4 (using a confidence interval of 99%).
Differences in urinary L/R ratios between different conditions were assessed using Wilcoxon signed ranks test.
Correlation plots comparing PLIER scores for all probe sets between different conditions were generated using R software.
Paired statistical analysis makes use of a single index to discriminate between different conditions, but it uses the information that data are paired.
The shotgun approach aims at comparing complete proteomes in terms of protein abundances between different conditions without any a priori use of an LC-MS workflow.
The magnitude of L r)- r is a measure for the degree of clustering and can be used for comparison between different conditions.
But, since those instruments are specific to a defined health condition, their use for comparisons between different conditions is limited [ 3].
These consistent probe sets, which passed this filter, were further used to calculate gene expression changes between different conditions.
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