Shimokawa Kazuro, Kodzius Rimantas, Matsumura Yonehiro, Hayashizaki Yoshihide
CSH Protoc. 2008 Feb 1;2008:pdb.prot4938. doi: 10.1101/pdb.prot4938.
INTRODUCTIONIn terms of cost per measurement, the use of DNA microarrays for comprehensive and quantitative expression measurements is vastly superior to other methods such as Northern blotting or quantitative reverse transcriptase polymerase chain reaction (QRT-PCR). However, the output values of DNA microarrays are not always highly reliable or accurate compared with other techniques, and the output data sometimes consist of measurements of relative expression (treated sample vs. untreated) rather than absolute expression values as desired. In effect, some measurements from some laboratories do not represent absolute expression values (such as the number of transcripts) and as such are experimentally deficient. To address the problem that some microarray data sets fail to reflect the number of mRNA molecules sufficiently in a given sample (i.e., fail to provide absolute expression levels), additional methods are required. The procedure described here provides a new method for converting microarray data to absolute expression values with the use of external data such as expressed sequence tags (ESTs) and cap analysis of gene expression (CAGE) tags.
