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David Andrew Eccles added subsection_Bootstrap_Sub_sampling_of__.tex
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\subsection{Bootstrap Sub-sampling of the Discovery Group}
\label{sec:meth-summ-bootstrapping}
A bootstrap sub-sampling method was then carried out, generating 100
subsample replicates of the discovery group, each replicate having 490
T1D cases and 364 NBS controls (i.e. retaining the same proportions as
the original 981 cases and 729 controls), sampled from the original
discovery set without replacement. The SNPs were then ranked by
$\chi^2$, and a \emph{bootstrap-consistent set} of 458 SNPs was
identified, each ranked in the top 5\% of SNPs (24501 SNPs) in every
bootstrap sub-sample (see
Figure~\ref{fig:sig-thy-bootstrap-consistency}-A). Most of these 458
SNPs had a maximum rank below 5000, whereas most of the remaining
489574 SNPs had a maximum rank above 350000 (see
Figure~\ref{fig:sig-thy-bootstrap-consistency}-B).
