A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays.
Publication
, Journal Article
Lee, C-J; Fu, D; Du, P; Jiang, H; Lin, SM; Kibbe, W
Published in: Int J Comput Biol Drug Des
2008
Out-of-memory problem was frequently encountered when processing thousands of CEL files using Bioconductor. We propose a divide-and-conquer strategy combined with randomised resampling to solve this problem. The CAMDA 2007 META-analysis data set which contains 5896 CEL files was used to test the approach on a typical commodity computer cluster by running established pre-processing algorithms for Affymetrix arrays in the Bioconductor package. The results were validated against a golden standard obtained by using a supercomputer. In addition to the performance improvement, the general divide-and-conquer strategy can be applied to any other normalisation algorithms without modifying the underlying implementation.
Duke Scholars
Published In
Int J Comput Biol Drug Des
DOI
ISSN
1756-0756
Publication Date
2008
Volume
1
Issue
4
Start / End Page
396 / 405
Location
England
Related Subject Headings
- Problem Solving
- Oligonucleotide Array Sequence Analysis
- Humans
- Equipment Design
- Computers
- Computer Storage Devices
- Computational Biology
- Biostatistics
- 3214 Pharmacology and pharmaceutical sciences
- 3102 Bioinformatics and computational biology
Citation
APA
Chicago
ICMJE
MLA
NLM
Lee, C.-J., Fu, D., Du, P., Jiang, H., Lin, S. M., & Kibbe, W. (2008). A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays. Int J Comput Biol Drug Des, 1(4), 396–405. https://doi.org/10.1504/ijcbdd.2008.022209
Lee, Chia-Ju, Dong Fu, Pan Du, Hongmei Jiang, Simon M. Lin, and Warren Kibbe. “A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays.” Int J Comput Biol Drug Des 1, no. 4 (2008): 396–405. https://doi.org/10.1504/ijcbdd.2008.022209.
Lee C-J, Fu D, Du P, Jiang H, Lin SM, Kibbe W. A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays. Int J Comput Biol Drug Des. 2008;1(4):396–405.
Lee, Chia-Ju, et al. “A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays.” Int J Comput Biol Drug Des, vol. 1, no. 4, 2008, pp. 396–405. Pubmed, doi:10.1504/ijcbdd.2008.022209.
Lee C-J, Fu D, Du P, Jiang H, Lin SM, Kibbe W. A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays. Int J Comput Biol Drug Des. 2008;1(4):396–405.
Published In
Int J Comput Biol Drug Des
DOI
ISSN
1756-0756
Publication Date
2008
Volume
1
Issue
4
Start / End Page
396 / 405
Location
England
Related Subject Headings
- Problem Solving
- Oligonucleotide Array Sequence Analysis
- Humans
- Equipment Design
- Computers
- Computer Storage Devices
- Computational Biology
- Biostatistics
- 3214 Pharmacology and pharmaceutical sciences
- 3102 Bioinformatics and computational biology