apt-probeset-genotype is a program for making genotype calls from Affymetrix SNP microarrays. It currently implements three different genotype calling algorithms: BRLMM (pronounced ”B-realm”) - a model based approach similar to the RLMM (pronounced ”realm”) model developed by Nusrat Rabbee and Terry Speed but with a Bayesian extension, hence the ”B”. Currently requires seed genotypes for every SNP and sample analyzed which it obtains via the DM algorithm, hence it requires the presence of MisMatch (MM) probes. ...

References in zbMATH (referenced in 8 articles )

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  1. Yang, Jiaqi; Zhang, Wei; Wu, Baolin: A note on statistical method for genotype calling of high-throughput single-nucleotide polymorphism arrays (2013)
  2. Yang, Hsin-Chou; Lin, Hsin-Chi; Kang, Meijyh; Chen, Chun-Houh; Lin, Chien-Wei; Li, Ling-Hui; Wu, Jer-Yuarn; Chen, Yuan-Tsong; Pan, Wen-Harn: SAQC: SNP array quality control (2011) ioport
  3. Bengtsson, Henrik; Neuvial, Pierre; Speed, Terence P.: Tumorboost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays (2010) ioport
  4. Greenman, Chris D.; Bignell, Graham; Butler, Adam; Edkins, Sarah; Hinton, Jon: PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data (2010)
  5. Rancoita, Paola M. V.; Hutter, Marcus; Bertoni, Francesco; Kwee, Ivo: An integrated Bayesian analysis of LOH and copy number data (2010) ioport
  6. Sampson, Joshua N.; Zhao, Hongyu: Genotyping and inflated type I error rate in genome-wide association case/control studies (2009) ioport
  7. Wren, Jonathan D.; Gusev, Yuriy; Isokpehi, Raphael D.; Berleant, Daniel; Braga-Neto, Ulisses; Wilkins, Dawn; Bridges, Susan: Proceedings of the 2009 midsouth computational biology and bioinformatics society (MCBIOS) conference (2009) ioport
  8. Scharpf, Robert B.; Parmigiani, Giovanni; Pevsner, Jonathan; Ruczinski, Ingo: Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays (2008)