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Exact(27)
The small fold changes found in the study, while statistically significant, were too low to be reliably confirmed via immunoblot [49].
Even though our analyses of differentially expressed genes and GO categories associated with RR practice meet widely accepted criteria for statistical significance, we were concerned about the relatively small fold changes that were observed (see Supplementary Methods).
We have also found a statistical association between expression of the individual 3D-signature genes and tumor ER status, though small fold changes suggest this may be of limited biological relevance (Table 2).
The derivation of the p-value reflects the degree of variance between biological replicates and thus is a measure of the confidence in assigning significance of small fold changes in gene expression.
Approximate standard deviation was set so that some lower fold change genes were differentially expressed, so we could test whether small fold changes were still detectable after batch correction.
In view of the small fold changes expected from complex tissues such as brain, an extensive biomathematical workup including RMA-based normalization, fitting with a linear model, statistical ANOVA-based evaluation, stringent filtering, and representation of individual transcript changes per brain region in a decision matrix were applied to suppress background and to reveal the consistent effects.
Similar(33)
Because we assigned significance to a relatively small fold change (1.5 fold) for quantification, we verified the regulation of two adipocytokines that changed by 1.5 fold by an independent, orthogonal method.
We further excluded all probes with a small fold change (less extreme than +/− 1.5 fold) which results in 750 probe sets.
These genes have relatively small fold change (1.25 – 1.5), but the combined increase of multiple genes in this pathway strongly suggests that the ER stress response is not insignificant.
For instance, a small fold change in some lowly expressed gene may have greater biological importance than a small fold change in some abundant gene.
The text has been edited to accurately reflect the small fold change.
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