Many of the genes in the pseudo libraries were not simulated as up-regulated, but will nevertheless be picked up in the sampling of the library due to a high or moderate expression value.
For clustering, data were filtered to include only genes that showed at least moderate expression (expression value greater than 5) and a range of expression values across all samples (only the top one-third of genes as ranked by the expression range) were used for the clustering analysis.
Lead author Mathew Guest, at Durham University, says: "With the vast majority of Christian students affirming a moderate expression of values in keeping with wider British culture, the Church faces a difficult decision about whether to adapt to changing times or risk permanently alienating an entire generation".
Low, moderate and high expression values are calculated on the basis of the microarray clones fluorescence intensity and correspond respectively to values lower than 3,000, comprise between 3,000 and 10,000 and higher than 10,000 arbitrary fluorescence units.
In particular, three samples (2, 6, 10) showed a silent expression of SPARC gene, while samples 1, 3, 5, 7 had a moderate expression of SPARC (value between 1- and 10-fold increase) compared to normal.
A moderate correlation was observed between microarray expression values and number of 454 reads.
The processed and normalized expression values were not normally distributed, but moderate deviations from normality have been found to have little effect on ANOVA F-tests [ 101].
This was associated with a biphasic transition from viscoelastic-liquid to viscoelastic-solid behavior such that aggregates behaved as viscoelastic-solids for moderate α5 expression levels and liquid-like for either higher or lower expression values.
One possible explanation was that after the actual expression values were dichotomized into barcoded values, the genes with weak or even moderate association to survival were discarded.
The LIMMA derived log expression values were fit to a linear model based on treatment, which moderated the resulting t statistics using the empirical Bayes method.
