The effect on PDFs and $\alpha_S(M_Z^2)$ due to changes in flavour scheme and higher twist contributions

I consider the effect on MSTW partons distribution functions (PDFs) due to changes in the choices of theoretical procedure used in the fit. I first consider using the 3-flavour fixed flavour number scheme instead of the standard general mass variable flavour number scheme used in the MSTW analysis. This results in the light quarks increasing at all relatively small $x$ values, the gluon distribution becoming smaller at high values of $x$ and larger at small $x$, the preferred value of the coupling constant $\alpha_S(M_Z^2)$ falling, particularly at NNLO, and the fit quality deteriorates. I also consider lowering the kinematic cut on $W^2$ for DIS data and simultaneously introducing higher twist terms which are fit to data. This results in much smaller effects on both PDFs and $\alpha_S(M_Z^2)$ than the scheme change, except for quarks at very high $x$. I show that the structure function one obtains from a fixed input set of PDFs using the fixed flavour scheme and variable flavour scheme differ significantly for $x \sim 0.01$ at high $Q^2$, and that this is due to the fact that in the fixed flavour scheme there is a slow convergence of large logarithmic terms of the form $(\alpha_S\ln(Q^2/m_c^2))^n$ relevant for this regime. I conclude that some of the most significant differences in PDF sets are largely due to the choice of flavour scheme used.