  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.
