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Open Access Research article

Does replication groups scoring reduce false positive rate in SNP interaction discovery?

Marko Toplak1, Tomaz Curk1, Janez Demsar1 and Blaz Zupan12*

Author Affiliations

1 Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000 Ljubljana, Slovenia

2 Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA

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BMC Genomics 2010, 11:58  doi:10.1186/1471-2164-11-58

Published: 22 January 2010

Additional files

Additional file 1:

Performance graphs for all data sets. Graphs presenting the dependency of false positive counts given the number of selected best candidate interactions for all 12 simulated and 5 GEO data sets.

Format: ZIP Size: 1.8MB Download file or display content in a new window

Open Data

Additional file 2:

Performance graphs obtained with bootstrap sampling. Graphs presenting the dependency of false positive counts given the number of selected best candidate interactions for all 12 simulated and 5 GEO data sets. In addition to direct scoring and scoring with replication groups we report results obtained with bootstrap sampling.

Format: ZIP Size: 741KB Download file

Open Data

Additional file 3:

Performance graphs for differently sized subsets of GSE6754. Performance graphs for data subsets of 100, 200, 500, 1000, 2000, and 5000 samples drawn from GSE6754.

Format: ZIP Size: 287KB Download file

Open Data

Additional file 4:

Source code and data sets. Source code and data sets needed to replicate the experiments.

Format: ZIP Size: 5.2MB Download file

Open Data