The present invention is directed to methods of determining a copy number of nucleic acids in a biological specimen. More specifically, the invention provides a method for determining an absolute copy number of a transcript or a plurality of transcripts of interest in a biological specimen the size of which is determined using an external control. The invention further provides a method for diagnosis and prognosis of diseases associated with changes in a transcript copy number by measuring an absolute copy number of the transcript. The invention also provides a kit for measuring absolute copy number of a transcript or a plurality of transcripts. The invention further provides a method of creating a quantitative 'fingerprint' of a disease-related gene expression pattern for screening to identify susceptibility to a disease, and disease diagnostic and prognostic purposes.
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