  I consider the effect on partons distribution functions (PDFs) of changes in
the theoretical procedure used in a PDF fit. I 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 most $x$ values, the gluon distribution becoming softer at
high values of $x$ and larger at small $x$, and the coupling constant
$\alpha_S(M_Z^2)$ falling, particularly at NNLO. The fit quality also
deteriorates.I also consider lowering the kinematic cut on $W^2$ for DIS data
and introducing higher twist terms which are fit to data. This results in much
smaller effects on both PDFs and $\alpha_S(M_Z^2)$, with changes generally
smaller than uncertainties, except for quarks at very high $x$. I show that the
fixed flavour scheme and variable flavour scheme structure functions differ
significantly for $x \sim 0.01$ at high $Q^2$. I demonstrate that in the fixed
flavour scheme there is a slow convergence of large logarithmic terms of the
form $(\alpha_S\ln(Q^2/m_c^2))^n$ in this regime. I conclude that some major
differences in PDF sets are largely due to the choice of flavour scheme used.
