Figure 2

Box plots for determining cut-offs for the presence or divergence of genes. Example of two different box plots of two different microarray slides (Sa07_010 and Sa07_015) constructed using GraphPad Prism5. ¹MRSA252 are the spots originating from MRSA252 and should give a signal for in the Cy5 dye; ² Non252 are the spots originating from the other six strains (N315, MW2, Mu50, NCTC8325, COL and MSSA476), which are absent in the MRSA252 and so should not yield a Cy5 signal. The box plots illustrate the log₂ of the raw intensity of the reference (Cy5) channel for the MRSA252 and the non-MRSA252 spots separately. The horizontal line in the box denotes the median of the intensity. The log₂ of the signal for 50% of the spots falls within the boxes and the dots account for the upper and lower 5% of the spots. These pictures clearly show that height of the raw intensity does not correlate with the presence or divergence of a gene. These box plots indicate highly variable intensities between different spots on the same microarray slide.