Resolution:
## 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
Fasold and Binder |