Title: Balancing false positives and false negatives for the detection of differential expression in malignancies
Authors: De Smet, Frank ×
Moreau, Yves
Engelen, Kristof
Timmerman, Dirk
Vergote, Ignace
De Moor, Bart #
Issue Date: Oct-2004
Publisher: Harcourt Publishers
Series Title: British Journal of Cancer vol:91 issue:6 pages:1160-1165
Abstract: A basic problem of microarray data analysis is to identify genes whose expression is affected by the distinction between malignancies with different properties. These genes are said to be differentially expressed. Differential expression can be detected by selecting the genes with P-values (derived using an appropriate hypothesis test) below a certain rejection level. This selection, however, is not possible without accepting some false positives and negatives since the two sets of P-values, associated with the genes whose expression is and is not affected by the distinction between the different malignancies, overlap. We describe a procedure for the study of differential expression in microarray data based on receiver-operating characteristic curves. This approach can be useful to select a rejection level that balances the number of false positives and negatives and to assess the degree of overlap between the two sets of P-values. Since this degree of overlap characterises the balance that can be reached between the number of false positives and negatives, this quantity can be seen as a quality measure of microarray data with respect to the detection of differential expression. As an example, we apply our method to data sets studying acute leukaemia.
ISSN: 0007-0920
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Gynaecological Oncology
Centre of Microbial and Plant Genetics
Section Woman - Miscellaneous (-)
Vesalius Research Centre (-)
Basic Research in Gynaecology Section (-)
ESAT - STADIUS, Stadius Centre for Dynamical Systems, Signal Processing and Data Analytics
Electrical Engineering - miscellaneous
Environment and Health - miscellaneous
× corresponding author
# (joint) last author

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