Figure 3.

Overview of microarray gene expression patterns in male and female Populus tremula trees from the Umeå Aspen collection. (a) Principal Component Analysis plot of the microarray data with samples classified by sex (male in blue, female in pink). The percentage variance explained by each component is shown in parenthesis for each axis. The female sample shown at the bottom left of the plot was classified as an outlier and excluded from statistical analyses. (b) Volcano plot of the negative log₁₀ p-value (y-axis) plotted against log₂-fold change (x-axis) showing the results of differential expression analysis comparing male to female trees assayed using whole-genome Agilent oligonucleotide microarrays. Technical noise was accounted for in the statistical model by including factors for slide and sub-array within slide and the effect of sex was tested after removal of variance due to those technical effects. Non-significant genes are coloured to indicate density, which is shaded from yellow (high) to blue (low). No genes were significant (note that 0.01 on the y-axis corresponds to a p-value of 0.977).