Marquez attended Sacramento City College before being chosen by the New York Yankees in the supplemental round as the 41st overall pick of 2004 Major League Baseball draft. Marquez was a compensation pick for losing David Wells to the San Diego Padres.\n', '

In 2005, Marquez played for the Single-A Charleston RiverDogs. Making a team leading 27 starts, he went 9-13 with an ERA of 3.42. Marquez was second on the team to Chase Wright in wins (9), innings pitched (​139 2⁄3), and strikeouts (107).\n', '

In 2007, Marquez played for the Double-A Trenton Thunder and was an Eastern League midseason All-Star for the team that year. Marquez went 15-9 with a 3.65 ERA for the Thunder. He led the league with 15 wins, was tied with 27 starts, was tied for second in innings pitched (155 1/3), tied for third in complete games (2), and was tenth in ERA (3.65).\n', '

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