The CRMA v2 method is implemented in the aroma.affymetrix package and the CalMaTe method in the calmate package. We will use an allele-specific version of the CRMA v2 method ( Bengtsson, Wirapati, and Speed, 2009) to estimate allele-specific copy numbers (ASCNs) at each SNP. , GSM318767.CELĪnalysis Allele-specific copy-number estimation (CRMA v2)

Dataīelow we will use the public GEO data set GSE12702: rawData/ Affymetrix and Illumina.Ĭontrary to the TumorBoost ( Bengtsson, Neuvial, and Speed, 2010), which requires a single pair of tumor-normal samples, the CalMaTe methods don't require matched normals, but instead it requires a large number of reference samples.įor more details, see Ortiz-Estevez, Aramburu, Bengtsson, Neuvial, and Rubio (2012). CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. PSCBS by Olshen, Bengtsson, Neuvial, Spellman, Olshen, and Seshan (2011)) for detecting changes between copy-number states in tumor studies including copy-neutral loss of heterozygosity (LOH). The resulting ASCNs are on average more accurate, which increases the power of segmentation methods (e.g. Vignette: CalMaTe - A calibration method to improve allele-specific copy number of SNP arrays for downstream segmentationĬalMaTe calibrates preprocessed allele-specific copy-number estimates (ASCNs) from DNA microarrays by controlling for SNP-specific allelic crosstalk.

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