We also performed sensitivity analyses on the final models using a more stringent (intensity score strong and at least 25% or more of cells showing evidence of overexpression) as well as a less stringent definition (intensity score of moderate or strong with at least 10% or more of cells showing evidence of overexpression) of positivity.
Possible reasons for this lower expression could be the growth conditions and/or the stringent intensity cutoff used for identification of expressed regions.
Comparison of the classification accuracy of highly discriminative 2829 probe sets (selected using MWT on cross-normalized signal intensity values with a stringent 100% accuracy criteria and a bootstrap p-value cut-off<0.05) with top-level 2829 probe sets identified by standard Wilcoxon sign ranked test (WT), EDGE, PAM, and student& 8217s t-test.
DOI: http://dx.doi.org/10.7554/eLife.01828.004 To focus our analysis, we used a stringent cut-off of a ninefold increase in HPL staining intensity, which resulted in 19 genes.
The Bonferroni corrected critical value was calculated by dividing alpha by the number of buckets used in the PCA, resulting in a stringent P value threshold for determination of statistically significant changes in resonance intensities between groups being compared.
To further breakdown the microarray data, a second method of analysis of the original signal intensities derived from the MAS software analysis was performed using a stringent P-value.
A stringent lower limit threshold was set at 3 standard deviations of the pixel intensities of the negative control spots, and images were screened for changes in expression values of at least 2-fold.
During the development phase, we performed replicate hybridizations of DNA from two different rice mutants (G650 and F1856), and determined that the use of a stringent log ratio [= log2 (mutant PM probe signal intensity/wild type PM probe signal intensity)] cutoff for a high proportion of probes within a probe set was almost equivalent to the use of a p-value cutoff.
Such high accuracy spectroscopy is shown to provide a stringent test of calculated potential energy and ab initio dipole moment surfaces, and therefore transition intensities calculated from first principles.
Consequently, generalizing statements postulating a stringent inhibition of BChl synthesis in marine aerobic anoxygenic photosynthetic bacteria even by low light intensities [e.g. 36], [37] have to be reconsidered.
