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\bibstyle{abbrvnat}
\citation{Golub}
\citation{hopach}
\citation{hopach2}
\citation{jsm}
\citation{sci}
\@writefile{toc}{\contentsline {section}{\numberline {1}Overview}{1}{section.1}}
\@writefile{toc}{\contentsline {section}{\numberline {2}Getting started}{1}{section.2}}
\@writefile{toc}{\contentsline {section}{\numberline {3}Introduction}{2}{section.3}}
\@writefile{toc}{\contentsline {section}{\numberline {4}HOPACH Clustering of Genes}{2}{section.4}}
\@writefile{toc}{\contentsline {section}{\numberline {5}Bootstrap Resampling}{3}{section.5}}
\@writefile{toc}{\contentsline {section}{\numberline {6}HOPACH Clustering of Arrays}{3}{section.6}}
\bibdata{hopach}
\@writefile{toc}{\contentsline {section}{\numberline {7}Output files}{4}{section.7}}
\@writefile{toc}{\contentsline {subsection}{\numberline {7.1}Gene clustering and bootstrap results table}{4}{subsection.7.1}}
\@writefile{toc}{\contentsline {subsection}{\numberline {7.2}Bootstrap fuzzy clustering in MapleTree}{4}{subsection.7.2}}
\@writefile{toc}{\contentsline {subsection}{\numberline {7.3}HOPACH hierarchical clustering in MapleTree}{4}{subsection.7.3}}
\@writefile{lof}{\contentsline {figure}{\numberline {1}{\ignorespaces The {\texttt  {dplot}} function orders the rows and columns of the distance matrix according to the final level of the {\texttt  {hopach}} hierarchical tree. Red represents small distance and white large distance.}}{5}{figure.1}}
\newlabel{image}{{1}{5}{HOPACH hierarchical clustering in MapleTree\relax }{figure.1}{}}
\@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces The {\texttt  {bootplot}} function makes a barplot of the bootstrap reappearance proportions for each gene and each cluster. These proportions can be viewed as fuzzy cluster memberships. Every cluster is represented by a different color. The genes are ordered by {\texttt  {hopach}} cluster, and then by bootstrap estimated membership within cluster on the vertical axis so that each gene is represented by a horizontal bar.}}{5}{figure.2}}
\newlabel{barplot}{{2}{5}{HOPACH hierarchical clustering in MapleTree\relax }{figure.2}{}}
