Significance analysis of microarrays

Abbreviation Bp, nucleotide base pairs cDNA, complementary DNA ChIP, chromatin Immunoprecipi-tation Cy5, cyanine 5-dCTP Cy3, cyanine 3-dCTP ESTs, expressed sequence tags FDR, false discovery rate MIAME, minimum information about a microarray experiment mRNA, RNA, messenger NIA, National Institutes of Aging RFUs, relative fluorescence units RT-PCR, reverse transcriptase polymerase chain reaction SAGE, serial analysis of gene expression SAM, significance analysis of microarrays... 

Tusher VG, Tibshirani R, Ghu G. 2001. Significance analysis of microarrays applied to ionizing radiation response. Proc Natl Acad Sci USA 98 5116. 

Instead of controlling the expected proportion of incorrect rejections, one might control the expected number of incorrect rejections. As explained by Dudoit et al. (2003), in essence this is what is achieved by the significance analysis of microarrays (SAM) methods of Efron et al. (2001) and Tusher et al. (2001). The issue of which error rate is the best to control in terms of leading to more discoveries of useful transcription factors is an on-going research project. 

Tusher, V.G., R. Tibshirani and G. Chu. Significant analysis of microarrays applied to the ionizing radiation... 

A number of ad hoc methods to analyze large biological data have been developed. They utilize the characteristics of the large biological data. For analyzing large data from microarray experiments, SAM (significance analysis of microarrays) (Tusher et al., 2001), newly developed, has been widely used. In fact, it resembles the... 

Tusher, V. Tibishirani, R. Chu, C. (2001). Significance Analysis of Microarrays Applied o Transcriptional Response to Ionizing Radiation. Proc. Natl. Acad. Sci, Vol. 98, pp. 5116-5121. 

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