Document Type
Article
Original Publication Date
2004
Journal/Book/Conference Title
BMC Bioinformatics
Volume
5
DOI of Original Publication
10.1186/1471-2105-5-60
Date of Submission
September 2014
Abstract
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® dataset, problems associated with applying the log2 transformation to absolute intensity data are demonstrated. Use of the spread-versus-level plot to identify an appropriate variance stabilizing transformation is presented. For the data presented, the spread-versus-level plot identified a power transformation that successfully stabilized the variance of probe set summaries.
Conclusion
The spread-versus-level plot is helpful to identify transformations for variance stabilization. This is robust against outliers and avoids assumption of models and maximizations.
Rights
© 2004 Archer et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
Is Part Of
VCU Biostatistics Publications
Comments
Originally published at http://dx.doi.org/10.1186/1471-2105-5-60