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Projects in 2004–2005

Applied Biosystems: Automated Analysis of Gene Expression Data

Henry Krieger

Biologists use a technique called real-time polymerase chain reaction (PCR) to collect gene expression data in large quantities. A potential use of this data is to help determine genes that reliably classify samples; however, complications can arise when the amount of data is large. Extracting information from large data sets often requires sophisticated mathematical techniques. We explore several methods, focusing our efforts on principal component analysis and δCt values, or measures of relative gene expression levels. Our current work involves several data sets, including studies regarding lymphoma, leukemia, and cranial mutations in mice. While none of our techniques identify genes that reliably classify patients in the lymphoma data set, we observe promising results with many of our techniques on the other data sets.


  • Jeff Brenion
  • Kevin Krogh
  • Theresa Poindexter
  • Ryan Riegel

Hewlett-Packard Labs: Printer Drift and Recalibration

Weiqing Gu

Today's digital color printers achieve a wide gamut of colors from the overlay of three to eight layers of ink. Ink is placed on the substrate/paper in different amounts to create a huge array of color mixtures. A standard procedure is to create a 3-D lookup table to determine the amounts of each ink that will produce a chosen color. This table is constructed by printing up to thousands of ink combinations on a chosen substrate/paper and measuring the resulting colors via a spectrophotometer. This information is used to plot the ink combinations within an internationally recognized color coordinate system, and then a regular grid of points is interpolated within this coordinate system to produce the lookup table.

Changes in temperature, paper quality, substrate, and even "printer drift" affect how varying ink combinations behave with one another, resulting in the lookup table no longer being accurate. A new lookup table must then be produced to recalibrate the printer. We intend to investigate ways to make this recalibration more efficient than current solutions.


  • Brianne Boatman
  • Durban Frazer
  • Jeff Hellrung
  • Katie Lewis