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The number of molecules in the unknown samples were determined and divided by the known number of cells in the qPCR template to obtain copy number per cell.
To obtain copy numbers, we calculated reads per million per kilobase for all open reading frames.
We developed a method to obtain copy number information from the Illumina Methylation27K BeadChip array (see Methods and Supplemental Material).
(Morrison et al, 2007) Fluorescence in situ hybridisation signals were enumerated in ⩾40 cells per specimen to obtain copy numbers for each locus, and 72 specimens yielded results for all six probes.
An integrated read summarization function, seqsumm, written in C++ and interfacing with the R code through Rcpp, makes seqCNA the only tool required to obtain copy number profiles from SAM alignment files (SAMtools [ 20] is necessary to read BAM files).
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To obtain copies of the publication, call Ayeshah Wiltshire at the Arts Council, (914 428-4220, extension 241.
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