Analysis of probe level patterns in Affymetrix microarray data

Background: Microarrays have been used extensively to analyze the expression profiles for thousands of genes in parallel. Most of the widely used methods for analyzing Affymetrix Genechip microarray data, including RMA, GCRMA and Model Based Expression Index (MBEI), summarize probe signal intensity data to generate a single measure of expression for each transcript on the array. In contrast, other methods are applied directly to probe intensities, negating the need for a summarization step. Results: In this study, we used the Affymetrix rat genome Genechip to explore variability in probe response patterns within transcripts. We considered a number of possible sources of variability in probe sets including probe location within the transcript, middle base pair of the probe sequence, probe overlap, sequence homology and affinity. Although affinity, middle base pair and probe location effects may be seen at the gross array level, these factors only account for a small proportion of the v...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Alexander C. Cambon, Abdelnaby Khalyfa, Nigel G. F. Cooper, Caryn M. Thompson
• Keywords: Affymetrix Genechip Microarray, BMCBI 2007, Genechip Microarray Data, Middle Base Pair