Patent ID: 7962291

Claim:
A computer-implemented method for identifying exons that are differentially spliced between at least a first and second sample comprising: (a) obtaining an exon intensity measurement for a first exon in a first gene in said first sample and in said second sample; (b) calculating a gene level measurement for said first gene in said first sample and in said second sample, wherein the gene level measurement for said first gene is a median normalized intensity value from all exons in said first gene in said first sample and the gene level measurement for said second sample is a median normalized intensity value from all exons in said first gene in said second sample; (c) calculating a first normalized intensity measurement for said first exon in said first sample and a second normalized intensity measurement for said first exon in said second sample by dividing the intensity measurements obtained in (a) by the gene level measurements obtained in step (b) wherein the exon intensity in said first sample is divided by the gene level measurement in said first sample and the exon intensity in said second sample is divided by the gene level measurement in said second sample; (d) calculating a splicing index measurement for said first exon, wherein the splicing index is equal to the log 2 of the normalized intensity for said first exon in said first sample divided by the normalized intensity for said first exon in said second sample, and wherein the calculating in steps (b), (c) and (d) is performed by a computer comprising a computer software product; and (e) identifying said first exon as being differentially spliced if the absolute value of the splicing index obtained in (d) is greater than a threshold value, wherein exon array background correction is performed by use of a background probe collection.