A natural log transformation of groundwater depth was tested to see if rescaling dataset variance would result in finer distinctions for regions of shallow groundwater.
Multivariate assemblage data highlighted similar directional shifts in dominance to Pavona varians and other Porites colonies (mainly P. lichen, and P. rus, Figure 2b, species-centered PCA, horizontal axis explained 48.5% of the dataset variance, vertical axis explained 18.3%).
These genes were ranked higher by the combined dataset because of their low inter-dataset variance.
The principal component 3, which separated the dose effect of MCSF, explained less than 8% of the dataset variance.
From the remaining data variance -after the removal of the first PC- a second PC that is completely uncorrelated with – i.e. orthogonal to – the first one is extracted, and accounts for the maximum possible remaining dataset variance.
Though in general the DASL-based approach is more reliable than the IVT-based approach for profiling degraded mRNA samples, our MDMR analyses suggest that RNA degradation and other factors still play important roles in determining dataset variance, thereby potentially confounding differential expression analyses.
We used a restrictive α value (α < 0.05) for which a given variable was allowed into the model and selected only final models that explained at least 20% of the dataset variance (R > 0.20) with a P value of the regression ANOVA less than 0.01.
But the performance of the statistics ignoring test dataset variances, FMean, GGlobal and GPooled dose not increase as much as the increment of sample size.
GMixBayes is modified from earlier GEO-adjusted methods in two aspects: estimation of prior variance using Gaussian mixture model and Bayesian integration of both testing and reference dataset variances.
This limited improvement in the hybrid scheme with GMixBayes is possibly because GMixBayes already incorporates the benefit of TReg in the level of statistical calculation through the Bayesian integration of test- and reference-dataset variances.
