New Spiked-In Probe Sets for the Affymetrix HGU-133A Latin Square Experiment

Monnie McGee, Southern Methodist University
Zhongxue Chen, University of Texas Southwestern Medical Center


The Affymetrix HGU-133A spike in data set has been used for determining the sensitivity and specificity of various methods for the analysis of microarray data. We show that there are 22 additional probe sets that should be considered as spikeins. We assign each proposed spiked-in probe set to a concentration group within the Latin Square design, and examine the effects of the additional spiked-in probe sets on methods of analysis currently in use.