Figure 3

Hook- and degradation hook (above) and tongs-plot (below) of two selected chip hybridization taken form the human body index data set (muscle, GEO accession numbers GSM176301 in part a and skin, GSM175967 in part b) referring to large and smaller degradation effects, respectively. Note that all plots use the same abscissa scaling (Σ, see Eq. (7)) which is related to the expression degree of the respective probes. The hook curve reveals the changing hybridization mode with increasing sigma: non-specific (N), mixed N and S (mix), specific (S), saturation (sat) and asymptotic (as) ranges. The degradation hook and the tongs-plot reveal the mean 3′/5′-intensity bias of the probes. The three branches of the tongs plot refer to three probes nearest to the 3′-end (upper branch), nearest to the 5′-end (lower branch) and located in the middle in-between (middle branch). Note that the different branches split maximally in the S-range of hybridization whereas no bias is observed in the N-range as predicted by theory (lines, see Eqs. (16) and (21) for the hook and tongs plot, respectively). The theoretical curves are calculated using the formulae given in the methodical section using the parameters given in the figure. The hook dimensions (α, ‘height’ of the hook, see Eq. (18); β, ‘width’ of the hook; Σ(0), ‘start’ point; M, ‘end’-point) are very similar for both arrays whereas the logarithmic 3′- and 5′-degradation levels (Eq. (24)) are markedly different. The size of the moving window is decreased towards the right end of the tongs plot to compensate the reduced number of probe sets in saturation range. As a consequence, the part of the curves beyond of the maximum is prone to increasing error