Subfig caption doesn't start at start of line

Question

I have a situation where the subfigure caption doesn't start at the start of the line. \captionsetup[table]{width=\textwidth} is added to try to have the caption take up the whole line rather than wrap at the boundaries of the table as recommended in Prevent wrapping of subtable captions in lyx.

%% LyX 1.6.7 created this file.  For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass[english]{article}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}

\makeatletter

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.
%% Because html converters don't know tabularnewline
\providecommand{\tabularnewline}{\\}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands.
\usepackage{caption}
\usepackage{subfig}
\captionsetup[table]{width=\textwidth}

\@ifundefined{showcaptionsetup}{}{%
 \PassOptionsToPackage{caption=false}{subfig}}
\usepackage{subfig}
\makeatother

\usepackage{babel}

\begin{document}
%
\begin{table}
\caption{Valleys in promoters of genes correlated with overexpression by breast
cancer subtype}


\label{tab:vlyTallyUniqVlyMtchCntrlOvrExp}

\subfloat[Number of valleys in the promoter region marking overexpresses genes
in breast cancer by subtype]{\begin{raggedright}

\par\end{raggedright}

\begin{raggedright}
\label{tab:vlyTallyUniqCombinedVlyMtchCntrlOvrExp}
\par\end{raggedright}

\raggedright{}\begin{tabular}{|c|c|c|c|}
\cline{3-4} 
\multicolumn{1}{c}{} &   & \multicolumn{2}{c|}{Over-expression}\tabularnewline
\cline{3-4} 
\multicolumn{1}{c}{} &  & Basal & Luminal \tabularnewline
\hline 
Marked & Basal  & 131  & 116\tabularnewline
\cline{2-4} 
Cell line & Luminal  & 100  & 104\tabularnewline
\hline
\end{tabular}}

\subfloat[Directly overlapping valleys in promoters of genes correlated with
overexpression by breast cancer subtype]{\begin{raggedright}

\par\end{raggedright}

\begin{raggedright}
\label{tab:vlyTallyUniqOverlappingVlyMtchCntrlOvrExp}
\par\end{raggedright}

\raggedright{}\begin{tabular}{|c|c|c|c|}
\cline{3-4} 
\multicolumn{1}{c}{} &   & \multicolumn{2}{c|}{Over-expression}\tabularnewline
\cline{3-4} 
\multicolumn{1}{c}{} &  & Basal & Luminal \tabularnewline
\hline 
Marked & Basal  & 26 & 18\tabularnewline
\cline{2-4} 
Cell line & Luminal  & 20 & 10\tabularnewline
\hline
\end{tabular}}
\end{table}




\end{document}

Answer 1

write after your \begin{figure} a \centering or in LyX mark the contents of the float and choose centering