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Extra info for ACM transactions on information systems (January)

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Replace each frequency 0 in the low-tag library with the lowest non-zero frequency of that tag in the scaled down libraries. Since the intention here is to solve the problem of the truncated libraries as conservatively as possible, we replace the zeros with the lowest possible value from the scaled down libraries, instead of, for instance, with a weighted average, or by replacing the values in a truncated library with the values of the most similar downscaled library in the same category. Of the 88 SAGE libraries studied, 28 were subjected to tag imputation.

AND LIPMAN, D. 1988. Improved tools for biological sequence comparison. In Proc. Natl. Acad. Sci. USA. Vol. 85. 2444–2448. RISSANEN, J. 1976. Generalized Kraft inequality and arithmetic coding. IBM J. Res. Dev. 20, 3, 198–203. , AND DELGRANGE, O. 1995. A guaranteed compression scheme for repetitive DNA sequences. Tech. Rep. IT–285, LIFL Lille I Univ. , AND RISSANEN, J. 2003a. DNA sequence compression using the normalized maximum likelihood model for discrete regression. In Proceedings of the Data Compression Conference.

23, No. 1, January 2005. A Methodology for Analyzing SAGE Libraries for Cancer Profiling ¨ JORG SANDER University of Alberta RAYMOND T. NG, MONICA C. SLEUMER, and MAN SAINT YUEN University of British Columbia and STEVEN J. JONES British Columbia Genome Sciences Centre Serial Analysis of Gene Expression (SAGE) has proven to be an important alternative to microarray techniques for global profiling of mRNA populations. We have developed preprocessing methodologies to address problems in analyzing SAGE data due to noise caused by sequencing error, normalization methodologies to account for libraries sampled at different depths, and missing tag imputation methodologies to aid in the analysis of poorly sampled SAGE libraries.

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ACM transactions on information systems (January) by Association for Computing Machinery


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