Two-sided student t-tests were used to determine relative differences between PDAC and benign samples, using the log ratios of metabolite versus thymine-D4 (internal standard, IS); FDR was estimated as V/R, where V is the expected number of false positives ([nominal p-value]*[number of comparisons made]) and R is the number of both true and false positives.
There are two ways of representing parallelism: the first is as a plot of measured concentrations for the patient samples against 1/dilution factor using log scales.
Using only dates from the log and the Choi algorithm yielded: 1) larger samples with valid data than using log dates and times, 2) similar wear-times as using log dates and times, 3) more wear-time (V, 48.1 min more; VM, 29.5 min more) than only log dates and Troiano algorithm.
Also, using log scale sampling, we verified that the chains were able to converge even if started with initial parameter values far from the final posterior mean values.
We calculated the Euclidean distance between samples using regularized-log transformed expression values to avoid that a few highly variable genes dominated the distance measure.
The diversity of the different components was reported as (a) Species Richness (SR), the total number of species or operational taxonomic units (OTUs) identified in each sample, (b) Shannon-Wiener information function (H', using log base 2), and (c) Margalef's index: (D = (S−1)/ln N), where S is the number of species and N is the number of individuals in the sample.
We demonstrate using log likelihood scores.
Two-sample t tests (using log-transformed data) were used to determine significant differences in gene expression between EGFR-mutant and -wild-type NSClinesll lines and between EGFR-transfected and parental MCF-7 cells (P values were two-sided).
In order to separate individual Sulfobacillus bins, a discrete bin containing putative members of the order Clostridiales, was isolated and further binned using log-normalized sample abundance patterns from 18 different samples, this time including fragments down to 1500 bp.
Drug response phenotypes (IC50 values) for both drugs were adjusted for ethnicity, gender and storage time of the 197 samples using linear regression (natural log transformation applied to IC50 values).
