Statistical comparison of two or more SAGE libraries: one tag at a time

Several statistical tests have been introduced for the comparison of serial analysis of gene expression (SAGE) libraries to quantitatively analyze the differential expression of genes. As each SAGE library is only one measurement, the necessary information on biological variation or experimental precision is lacking. Therefore, each test includes its own approach to derive such a variance measure from the data set or a theoretical distribution. Because the confidence in tag counts depends on the library size, a test between two or more libraries should be based on original tag counts. When groups of libraries are compared, the test should determine that the proportion of a specific tag in all libraries is the same (null hypothesis), but also offer the possibility to detect specific differences between individual libraries and groups of libraries. The Z-test and the G-test encompass these characteristics and are described for the comparison of two libraries and (two or more) groups of libraries, respectively.