Model-based variance-stabilizing transformation for Illumina microarray data

By Simon M. Lin, Pan Du, Wolfgang Huber, Warren A. Kibbe. Nucleic Acids Research, 2008

587 citations recorded by the source corpus.

Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit the performance of subsequent statistical modeling and inference. Due to the often limited number of technical replicates for Affymetrix and cDNA arrays, achieving variance stabilization can be difficult. Although the Illumina microarray platform provides a larger number of technical replicates on each array (usually over 30 randomly distributed beads per probe), these replicates have not been leveraged in the current log2 data transformation process. We devised a variance-stabilizing transformation (VST) method that takes advantage of the technical replicates available on an Illumina microarray. We have compared VST with log2 and Variance-stabilizing normalization (VSN) by using the Kruglyak bead-level data (2006) and Barnes titration data (2005). The results of the Kruglyak data suggest that VST stabilizes variances of bead-replicates within an array. The results of the Barnes data show that VST can improve the detection of differentially expressed genes and reduce false-positive identifications. We conclude that although both VST and VSN are built upon the same model of measurement noise, VST stabilizes the variance better and more efficiently for the Illumina platform by leveraging the availability of a larger number of within-array replicates. The algorithms and Supplementary Data are included in the lumi package of Bioconductor, available at: www.bioconductor.org.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/54810420accc9141460e47aa8d2d1ae04189365f

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Citations in the corpus

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis (2010, methodology): “Titration data has been widely used to evaluate the performance of new methods for analyzing mRNA expression microarrays [16,17].”
lumi: a pipeline for processing Illumina microarray (2008, methodology): “BeadExplorer) in Bioconductor to extend functionalities provided by the Illumina LIMS software named BeadStudio.”
Genome sequence-based species delimitation with confidence intervals and improved distance functions (2013, methodology): “58–79) and distinct data transformations [21,22] has frequently been recommended.”