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A probe-level model for analysis of GeneChip gene-expression data is presented which identified more than 10,000 single-feature polymorphisms (SFP) between two barley genotypes. The method has good sensitivity, as 67% of known single-nucleotide polymorphisms (SNP) were called as SFPs. This method is applicable to all oligonucleotide microarray data, accounts for SNP effects in gene-expression data and represents an efficient and versatile approach for highly parallel marker identification in large genomes.
Rostoks, N., Borevitz, J. O., Hedley, P. E., Russell, J., Mudie, S., Morris, J., … Waugh, R. (2005). Single-feature polymorphism discovery in the barley transcriptome. Genome Biology, 6(6). https://doi.org/10.1186/gb-2005-6-6-r54