A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays

doi:10.1186/1471-2105-8-434

BMC Bioinformatics

Volume 8

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Torring N
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Methodology article

A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays

Philippe Lamy¹ , Claus L Andersen² , Lars Dyrskjot² , Niels Torring² and Carsten Wiuf¹^,2

¹Bioinformatics Research Center, University of Aarhus, Hoegh-Guldbergsgade 10, Bldg 1090, 8000 Aarhus C, Denmark

²Molecular Diagnostic Laboratory, Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, 8200 Aarhus N, Denmark

author email corresponding author email

BMC Bioinformatics 2007, 8:434doi:10.1186/1471-2105-8-434


Published:	9 November 2007

Additional files

Additional File 1:

Linear relationship between mean intensities. The figure shows the average intensities for 1 copy of an allele (blue) and the average intensities for 2 copies of an allele (blue) plotted against the estimated mean intensities for 1 copy, using the model described in [8]. The parameter c1 is the intercept of the top line and c₂is the slope, see equation 2. The slope of the bottom line is 1 and the intercept 0.

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Additional File 2:

Histograms of allelic intensities for the HapMap data. The figure shows the histograms of the normalized intensities corresponding to 0, 1 or 2 copies.

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