Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals

Background: The usefulness of log2 transformation for cDNA microarray data has led to its widespread application to Affymetrix data. For Affymetrix data, where absolute intensities are indicative of number of transcripts, there is a systematic relationship between variance and magnitude of measurements. Application of the log2 transformation expands the scale of genes with low intensities while compressing the scale of genes with higher intensities thus reversing the mean by variance relationship. The usefulness of these transformations needs to be examined. Results: Using an Affymetrix GeneChip

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Kellie J. Archer, Catherine I. Dumur, Viswanathan Ramakrishnan
• Keywords: Affymetrix, BMCBI 2004, Log2 Transformation, Spread-versus-level Plot