If one wish to obtain the maximum performance for Types in the same truly single-array approach using CRMA v2, e.g. Slightly less good copy number estimates, to also process older chip This means that the results will be identical regardless whether arrays are processed in batches or separately, which is especially convenient when new samples arrives over time. Calculation of full-resolution (raw) total copy numbers, e.g.Ĭ = theta/thetaR, where theta and thetaR are probe summaries (chipĮffects) for the test sample and reference.Ī major advantage of CRMA v2 compared to CRMA v1 ( Bengtsson, Irizarry, Carvalho, and Speed, 2008), is that especially for GenomeWideSNP_5 and GenomeWideSNP_6 it is a truly single-array preprocessing method. Normalization for PCR fragment-length effects on summary signals.Robust probe-summarization on replicated PMs with PM=PMA+PMB for SNPs.Normalization for 25-mer nucleotide-position probe sequence effects.Calibration for crosstalk between allele probe pairs (PMA, PMB).That provides full-resolution raw total copy-number estimates, by the The CRMA v2 method is a preprocessing and probe summarization method If you wish to run CRMA v2 without going through the details, see Will be done one by one and the output of each step will be discussed. (CNs) in aroma.affymetrix according to the CRMA v2 method described inīengtsson, Wirapati, and Speed (2009). This document describes in detail how to estimate total copy numbers Vignette: Estimation of total copy numbers using the CRMA v2 method (10K-CytoScanHD)
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