Comparing Summaries of High Density Oligonucleotide

Array Probe Level Data.

Rafael A. Irizarry,

John Hopkins School of Public Health

In this talk we report some exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip system. We then compare various competing summaries of these data which are used as expression measures. Our analyses make use of four data sets: two small experimental studies consisting of 8 RGU34A chips and 5 MGU74A mouse chips, respectively; part of the data from an extensive spike-in study

conducted by Gene Logic and the Genetics Institute involving about 95 HGU95A chips; and part of a dilution study conducted by Gene Logic involving 75 HGU95A chips.