NDLI: Comparison of different approaches for comparative genetic analysis using microarray hybridization

Content Provider	Springer Nature Link
Author	Pin, Carmen Reuter, Mark Pearson, Bruce Friis, Lorna Overweg, Karin Baranyi, József Wells, Jerry
Copyright Year	2006
Abstract	A robust analysis of comparative genomic microarray data is critical for meaningful genomic comparison studies. In this paper, we compare our method (implemented in a new software tool, GENCOM, freely available at http://www.ifr.ac.uk/safety/gencom ) with three commonly used analysis methods: GACK (freely available at http://falkow.stanford.edu ), an empirical cut-off value of twofold difference between the fluorescence intensities after LOWESS normalization or after AVERAGE normalization in which the fluorescence intensity is divided by the average fluorescence intensity of the entire data set. Each method was tested using data sets from real experiments with prior knowledge of conserved and divergent genes. GENCOM and GACK were superior when a high proportion of genes were divergent. GENCOM was the most suitable method for the data set in which the relationship between the fluorescence intensities was not linear. GENCOM has proved robust in an analysis of all the data sets tested.
Starting Page	852
Ending Page	859
Page Count	8
File Format	PDF
ISSN	01757598
Journal	Applied Microbiology and Biotechnology
Volume Number	72
Issue Number	4
e-ISSN	14320614
Language	English
Publisher	Springer-Verlag
Publisher Date	2006-08-25
Publisher Place	Berlin, Heidelberg
Access Restriction	Subscribed
Subject Keyword	Microarrays Bioinformatics Genetic analysis Genomotyping Microbial Genetics and Genomics Microbiology Biotechnology
Content Type	Text
Resource Type	Article
Subject	Medicine Applied Microbiology and Biotechnology Biotechnology

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